diff --git a/CHANGELOG.md b/CHANGELOG.md
index eb0fa98..732c405 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,7 @@
 **Changed**
 - Install Jupytext from source on MyBinder to avoid cache issues (#567)
 - Skip the tests that execute a notebook on Windows to avoid timeout issues (#489)
+- The `# %%` cell marker has the same indentation as the first line in the cell (#562)
 
 **Fixed**
 - Configured coverage targets in `codecov.yml`
diff --git a/jupytext/cell_reader.py b/jupytext/cell_reader.py
index b3d3de7..627d58b 100644
--- a/jupytext/cell_reader.py
+++ b/jupytext/cell_reader.py
@@ -747,9 +747,9 @@ class DoublePercentScriptCellReader(LightScriptCellReader):
         script = _SCRIPT_EXTENSIONS[self.ext]
         self.default_language = default_language or script["language"]
         self.comment = script["comment"]
-        self.start_code_re = re.compile(r"^{}\s*%%(%*)\s(.*)$".format(self.comment))
+        self.start_code_re = re.compile(r"^\s*{}\s*%%(%*)\s(.*)$".format(self.comment))
         self.alternative_start_code_re = re.compile(
-            r"^{}\s*(%%|<codecell>|In\[[0-9 ]*\]:?)\s*$".format(self.comment)
+            r"^\s*{}\s*(%%|<codecell>|In\[[0-9 ]*\]:?)\s*$".format(self.comment)
         )
         self.explicit_soc = True
 
diff --git a/jupytext/cell_to_text.py b/jupytext/cell_to_text.py
index 369036c..b9a4f9a 100644
--- a/jupytext/cell_to_text.py
+++ b/jupytext/cell_to_text.py
@@ -457,10 +457,18 @@ class DoublePercentCellExporter(BaseCellExporter):  # pylint: disable=W0223
         options = metadata_to_double_percent_options(
             self.metadata, self.cell_metadata_json
         )
+        indent = ""
+        if self.is_code() and active and self.source:
+            first_line = self.source[0]
+            if first_line.strip():
+                left_space = re.compile(r"^(\s*)").match(first_line)
+                if left_space:
+                    indent = left_space.groups()[0]
+
         if options.startswith("%") or not options:
-            lines = [self.comment + " %%" + options]
+            lines = [indent + self.comment + " %%" + options]
         else:
-            lines = [self.comment + " %% " + options]
+            lines = [indent + self.comment + " %% " + options]
 
         if self.is_code() and active:
             source = copy(self.source)
diff --git a/jupytext/version.py b/jupytext/version.py
index b6d1df7..5580906 100644
--- a/jupytext/version.py
+++ b/jupytext/version.py
@@ -1,3 +1,3 @@
 """Jupytext's version number"""
 
-__version__ = "1.5.2"
+__version__ = "1.6.0-dev"

Black interferes with py:percent format in indented code blocks.
I am having an issue where py:percent notebooks that have cells divided within an if statement get destroyed by black when using --pipe black

``` 
# %%
if __name__ == '__main__':
     print(1)
# %%
     print(2)
```

gets reformatted into the following, which is not equivalent 

``` 
# %%
if __name__ == '__main__':
     print(1)
     # %%
     print(2)
```

For example, when running the following.

jupytext --to notebook test.py 
jupytext --to py:percent --pipe black test.ipynb

Will cause all cells that contain only indented code to be merged into one giant cell. Are they any formats / workarounds to ensure black does not destroy the scripts like so? Or are there any relevant settings that jupytext can set that will resolve this issue?

diff --git a/tests/test_read_simple_percent.py b/tests/test_read_simple_percent.py
index 60839e8..bfc79ff 100644
--- a/tests/test_read_simple_percent.py
+++ b/tests/test_read_simple_percent.py
@@ -502,3 +502,32 @@ def test_docstring_with_quadruple_quote(
     py = jupytext.writes(nb, "py:percent")
     nb2 = jupytext.reads(py, "py")
     compare_notebooks(nb2, nb)
+
+
+def test_cell_marker_has_same_indentation_as_code(
+    text="""# %%
+if __name__ == '__main__':
+    print(1)
+
+    # %%
+    # INDENTED COMMENT
+    print(2)
+""",
+    nb_expected=new_notebook(
+        cells=[
+            new_code_cell(
+                """if __name__ == '__main__':
+    print(1)"""
+            ),
+            new_code_cell(
+                """    # INDENTED COMMENT
+    print(2)"""
+            ),
+        ]
+    ),
+):
+    """The cell marker should have the same indentation as the first code line. See issue #562"""
+    nb_actual = jupytext.reads(text, fmt="py:percent")
+    compare_notebooks(nb_actual, nb_expected)
+    text_actual = jupytext.writes(nb_actual, fmt="py:percent")
+    compare(text_actual, text)

environment.yml
pip install -e .
parse_log_pytest
environment.yml
pytest pytest-cov flake8 pre-commit pytest
3.7
pytest --no-header -rA --tb=line --color=no -p no:cacheprovider -W ignore::DeprecationWarning
alabaster @ file:///home/ktietz/src/ci/alabaster_1611921544520/work
anyio @ file:///tmp/build/80754af9/anyio_1644481697509/work/dist
argon2-cffi @ file:///opt/conda/conda-bld/argon2-cffi_1645000214183/work
argon2-cffi-bindings @ file:///tmp/build/80754af9/argon2-cffi-bindings_1644569681205/work
astroid @ file:///croot/astroid_1676904296642/work
attrs @ file:///croot/attrs_1668696182826/work
autopep8 @ file:///opt/conda/conda-bld/autopep8_1650463822033/work
Babel @ file:///croot/babel_1671781930836/work
backcall @ file:///home/ktietz/src/ci/backcall_1611930011877/work
beautifulsoup4 @ file:///opt/conda/conda-bld/beautifulsoup4_1650462163268/work
black @ file:///opt/conda/conda-bld/black_1660237809219/work
bleach @ file:///opt/conda/conda-bld/bleach_1641577558959/work
brotlipy==0.7.0
certifi @ file:///croot/certifi_1671487769961/work/certifi
cffi @ file:///croot/cffi_1670423208954/work
cfgv @ file:///opt/conda/conda-bld/cfgv_1663174654333/work
charset-normalizer @ file:///tmp/build/80754af9/charset-normalizer_1630003229654/work
click @ file:///tmp/build/80754af9/click_1646056591685/work
cmarkgfm @ file:///tmp/build/80754af9/cmarkgfm_1613500761843/work
colorama @ file:///croot/colorama_1672386526460/work
commonmark @ file:///Users/ktietz/demo/mc3/conda-bld/commonmark_1630649545323/work
coverage @ file:///tmp/build/80754af9/coverage_1645520980410/work
cryptography @ file:///croot/cryptography_1677533068310/work
cycler @ file:///tmp/build/80754af9/cycler_1637851556182/work
debugpy @ file:///tmp/build/80754af9/debugpy_1637091426235/work
decorator @ file:///opt/conda/conda-bld/decorator_1643638310831/work
defusedxml @ file:///tmp/build/80754af9/defusedxml_1615228127516/work
dill @ file:///croot/dill_1667919592856/work
distlib @ file:///croot/distlib_1673477531104/work
docutils @ file:///opt/conda/conda-bld/docutils_1657175430858/work
entrypoints @ file:///tmp/build/80754af9/entrypoints_1649908585034/work
execnet @ file:///tmp/build/80754af9/execnet_1623921183358/work
fastjsonschema @ file:///opt/conda/conda-bld/python-fastjsonschema_1661371079312/work
filelock @ file:///croot/filelock_1672387128942/work
flake8 @ file:///opt/conda/conda-bld/flake8_1648129545443/work
flit_core @ file:///opt/conda/conda-bld/flit-core_1644941570762/work/source/flit_core
fonttools==4.25.0
future @ file:///croot/future_1677599870788/work
identify @ file:///opt/conda/conda-bld/identify_1663193176610/work
idna @ file:///croot/idna_1666125576474/work
imagesize @ file:///opt/conda/conda-bld/imagesize_1657179498843/work
importlib-metadata==4.2.0
importlib-resources @ file:///tmp/build/80754af9/importlib_resources_1625135880749/work
iniconfig @ file:///home/linux1/recipes/ci/iniconfig_1610983019677/work
ipykernel @ file:///opt/conda/conda-bld/ipykernel_1662361798230/work
ipython @ file:///tmp/abs_94gruux8u8/croots/recipe/ipython_1659529858706/work
ipython-genutils @ file:///tmp/build/80754af9/ipython_genutils_1606773439826/work
ipywidgets @ file:///croot/ipywidgets_1701289330913/work
isort @ file:///tmp/build/80754af9/isort_1628603791788/work
jedi @ file:///tmp/build/80754af9/jedi_1644299024593/work
jeepney @ file:///tmp/build/80754af9/jeepney_1627537048313/work
Jinja2 @ file:///croot/jinja2_1666908132255/work
json5 @ file:///tmp/build/80754af9/json5_1624432770122/work
jsonschema @ file:///croot/jsonschema_1676558650973/work
jupyter @ file:///tmp/abs_33h4eoipez/croots/recipe/jupyter_1659349046347/work
jupyter-console @ file:///croot/jupyter_console_1671541909316/work
jupyter-contrib-core @ file:///home/conda/feedstock_root/build_artifacts/jupyter_contrib_core_1657548529421/work
jupyter-contrib-nbextensions @ file:///home/conda/feedstock_root/build_artifacts/jupyter_contrib_nbextensions_1670068802953/work
jupyter-highlight-selected-word @ file:///home/conda/feedstock_root/build_artifacts/jupyter_highlight_selected_word_1695322379939/work
jupyter-latex-envs @ file:///home/conda/feedstock_root/build_artifacts/jupyter_latex_envs_1614852190293/work
jupyter-nbextensions-configurator @ file:///home/conda/feedstock_root/build_artifacts/jupyter_nbextensions_configurator_1670793770953/work
jupyter-server @ file:///croot/jupyter_server_1671707632269/work
jupyter_client @ file:///croot/jupyter_client_1676329080601/work
jupyter_core @ file:///croot/jupyter_core_1668084443243/work
jupyterlab @ file:///croot/jupyterlab_1675354114448/work
jupyterlab-pygments @ file:///tmp/build/80754af9/jupyterlab_pygments_1601490720602/work
jupyterlab-widgets @ file:///tmp/build/80754af9/jupyterlab_widgets_1609884341231/work
jupyterlab_server @ file:///croot/jupyterlab_server_1677143054853/work
-e git+https://github.com/mwouts/jupytext.git@a8992b01db6d9c0133d8d3dc3175c597e8028f51#egg=jupytext
keyring @ file:///tmp/build/80754af9/keyring_1638531257242/work
kiwisolver @ file:///croot/kiwisolver_1672387140495/work
lazy-object-proxy @ file:///tmp/build/80754af9/lazy-object-proxy_1616529086024/work
lxml @ file:///opt/conda/conda-bld/lxml_1657545139709/work
markdown-it-py @ file:///opt/conda/conda-bld/markdown-it-py_1659718716158/work
MarkupSafe @ file:///opt/conda/conda-bld/markupsafe_1654597864307/work
matplotlib @ file:///croot/matplotlib-suite_1667356714455/work
matplotlib-inline @ file:///opt/conda/conda-bld/matplotlib-inline_1662014470464/work
mccabe==0.6.1
mdit-py-plugins @ file:///home/conda/feedstock_root/build_artifacts/mdit-py-plugins_1677788301074/work
mdurl @ file:///opt/conda/conda-bld/mdurl_1659716024347/work
mistune @ file:///tmp/build/80754af9/mistune_1594373098390/work
munkres==1.1.4
mypy-extensions==0.4.3
myst-parser @ file:///home/conda/feedstock_root/build_artifacts/myst-parser_1678230311298/work
nbclassic @ file:///croot/nbclassic_1676902904845/work
nbclient @ file:///tmp/build/80754af9/nbclient_1650308370114/work
nbconvert @ file:///croot/nbconvert_1668450669124/work
nbformat @ file:///croot/nbformat_1670352325207/work
nest-asyncio @ file:///croot/nest-asyncio_1672387112409/work
nodeenv @ file:///opt/conda/conda-bld/nodeenv_1663181097182/work
notebook @ file:///croot/notebook_1668179881751/work
notebook_shim @ file:///croot/notebook-shim_1668160579331/work
numpy @ file:///opt/conda/conda-bld/numpy_and_numpy_base_1653915516269/work
packaging @ file:///croot/packaging_1671697413597/work
pandocfilters @ file:///opt/conda/conda-bld/pandocfilters_1643405455980/work
parso @ file:///opt/conda/conda-bld/parso_1641458642106/work
pathspec @ file:///croot/pathspec_1674681560568/work
pexpect @ file:///tmp/build/80754af9/pexpect_1605563209008/work
pickleshare @ file:///tmp/build/80754af9/pickleshare_1606932040724/work
Pillow==9.4.0
pkginfo @ file:///croot/pkginfo_1666725041340/work
pkgutil_resolve_name @ file:///opt/conda/conda-bld/pkgutil-resolve-name_1661463321198/work
platformdirs @ file:///opt/conda/conda-bld/platformdirs_1662711380096/work
pluggy @ file:///tmp/build/80754af9/pluggy_1648042572264/work
ply==3.11
pre-commit @ file:///opt/conda/conda-bld/pre-commit_1663261387970/work
prometheus-client @ file:///tmp/abs_d3zeliano1/croots/recipe/prometheus_client_1659455100375/work
prompt-toolkit @ file:///croot/prompt-toolkit_1672387306916/work
psutil @ file:///opt/conda/conda-bld/psutil_1656431268089/work
ptyprocess @ file:///tmp/build/80754af9/ptyprocess_1609355006118/work/dist/ptyprocess-0.7.0-py2.py3-none-any.whl
py @ file:///opt/conda/conda-bld/py_1644396412707/work
pycodestyle @ file:///tmp/build/80754af9/pycodestyle_1636635402688/work
pycparser @ file:///tmp/build/80754af9/pycparser_1636541352034/work
pyflakes @ file:///tmp/build/80754af9/pyflakes_1636644436481/work
Pygments @ file:///opt/conda/conda-bld/pygments_1644249106324/work
pylint @ file:///croot/pylint_1676919896363/work
pyOpenSSL @ file:///croot/pyopenssl_1677607685877/work
pyparsing @ file:///opt/conda/conda-bld/pyparsing_1661452539315/work
PyQt5-sip==12.11.0
pyrsistent @ file:///tmp/build/80754af9/pyrsistent_1636098896055/work
PySocks @ file:///tmp/build/80754af9/pysocks_1594394576006/work
pytest==7.1.2
pytest-cov @ file:///tmp/build/80754af9/pytest-cov_1637159997573/work
pytest-forked @ file:///home/ktietz/src/ci_ipy2/pytest-forked_1612520962786/work
pytest-xdist @ file:///opt/conda/conda-bld/pytest-xdist_1651785087298/work
python-dateutil @ file:///tmp/build/80754af9/python-dateutil_1626374649649/work
pytz @ file:///croot/pytz_1671697431263/work
PyYAML @ file:///croot/pyyaml_1670514731622/work
pyzmq @ file:///opt/conda/conda-bld/pyzmq_1657724186960/work
qtconsole @ file:///croot/qtconsole_1674008428467/work
QtPy @ file:///opt/conda/conda-bld/qtpy_1662014892439/work
readme-renderer @ file:///tmp/build/80754af9/readme_renderer_1613502053370/work
recommonmark @ file:///Users/ktietz/demo/mc3/conda-bld/recommonmark_1629466645250/work
requests @ file:///opt/conda/conda-bld/requests_1657734628632/work
requests-toolbelt @ file:///Users/ktietz/demo/mc3/conda-bld/requests-toolbelt_1629456163440/work
rfc3986 @ file:///Users/ktietz/demo/mc3/conda-bld/rfc3986_1629478296451/work
SecretStorage @ file:///tmp/build/80754af9/secretstorage_1614022884812/work
Send2Trash @ file:///tmp/build/80754af9/send2trash_1632406701022/work
sip @ file:///tmp/abs_44cd77b_pu/croots/recipe/sip_1659012365470/work
six @ file:///tmp/build/80754af9/six_1644875935023/work
sniffio @ file:///tmp/build/80754af9/sniffio_1614030478629/work
snowballstemmer @ file:///tmp/build/80754af9/snowballstemmer_1637937080595/work
soupsieve @ file:///croot/soupsieve_1666296392845/work
Sphinx @ file:///opt/conda/conda-bld/sphinx_1657784123546/work
sphinx-copybutton==0.5.2
sphinx-gallery @ file:///home/conda/feedstock_root/build_artifacts/sphinx-gallery_1700542355088/work
sphinx-rtd-theme==2.0.0
sphinxcontrib-applehelp @ file:///home/ktietz/src/ci/sphinxcontrib-applehelp_1611920841464/work
sphinxcontrib-devhelp @ file:///home/ktietz/src/ci/sphinxcontrib-devhelp_1611920923094/work
sphinxcontrib-htmlhelp @ file:///tmp/build/80754af9/sphinxcontrib-htmlhelp_1623945626792/work
sphinxcontrib-jquery==4.1
sphinxcontrib-jsmath @ file:///home/ktietz/src/ci/sphinxcontrib-jsmath_1611920942228/work
sphinxcontrib-qthelp @ file:///home/ktietz/src/ci/sphinxcontrib-qthelp_1611921055322/work
sphinxcontrib-serializinghtml @ file:///tmp/build/80754af9/sphinxcontrib-serializinghtml_1624451540180/work
terminado @ file:///croot/terminado_1671751832461/work
tinycss2 @ file:///croot/tinycss2_1668168815555/work
toml @ file:///tmp/build/80754af9/toml_1616166611790/work
tomli @ file:///opt/conda/conda-bld/tomli_1657175507142/work
tomlkit @ file:///tmp/abs_56_0lnnq5x/croots/recipe/tomlkit_1658946880479/work
tornado @ file:///opt/conda/conda-bld/tornado_1662061693373/work
tqdm @ file:///opt/conda/conda-bld/tqdm_1664392687731/work
traitlets @ file:///croot/traitlets_1671143879854/work
twine @ file:///croot/twine_1690451545513/work
typed-ast @ file:///tmp/build/80754af9/typed-ast_1624953380449/work
typing_extensions @ file:///croot/typing_extensions_1669924550328/work
ukkonen @ file:///opt/conda/conda-bld/ukkonen_1663174535639/work
urllib3 @ file:///croot/urllib3_1673575502006/work
virtualenv==20.16.2
wcwidth @ file:///Users/ktietz/demo/mc3/conda-bld/wcwidth_1629357192024/work
webencodings==0.5.1
websocket-client @ file:///tmp/build/80754af9/websocket-client_1614804260725/work
widgetsnbextension @ file:///tmp/build/80754af9/widgetsnbextension_1645009354203/work
wrapt @ file:///tmp/abs_c335821b-6e43-4504-9816-b1a52d3d3e1eel6uae8l/croots/recipe/wrapt_1657814400492/work
zipp @ file:///croot/zipp_1672387121353/work

name: jupytext
channels:
  - defaults
  - https://repo.anaconda.com/pkgs/main
  - https://repo.anaconda.com/pkgs/r
  - conda-forge
dependencies:
  - _libgcc_mutex=0.1=main
  - _openmp_mutex=5.1=1_gnu
  - alabaster=0.7.12=pyhd3eb1b0_0
  - anyio=3.5.0=py37h06a4308_0
  - argon2-cffi=21.3.0=pyhd3eb1b0_0
  - argon2-cffi-bindings=21.2.0=py37h7f8727e_0
  - astroid=2.14.2=py37h06a4308_0
  - attrs=22.1.0=py37h06a4308_0
  - autopep8=1.6.0=pyhd3eb1b0_1
  - babel=2.11.0=py37h06a4308_0
  - backcall=0.2.0=pyhd3eb1b0_0
  - beautifulsoup4=4.11.1=py37h06a4308_0
  - black=22.6.0=py37h06a4308_0
  - blas=1.0=openblas
  - bleach=4.1.0=pyhd3eb1b0_0
  - brotli=1.0.9=h5eee18b_9
  - brotli-bin=1.0.9=h5eee18b_9
  - brotlipy=0.7.0=py37h27cfd23_1003
  - bzip2=1.0.8=h5eee18b_6
  - ca-certificates=2025.2.25=h06a4308_0
  - certifi=2022.12.7=py37h06a4308_0
  - cffi=1.15.1=py37h5eee18b_3
  - cfgv=3.3.1=py37h06a4308_0
  - charset-normalizer=2.0.4=pyhd3eb1b0_0
  - click=8.0.4=py37h06a4308_0
  - cmarkgfm=0.4.2=py37h27cfd23_0
  - colorama=0.4.6=py37h06a4308_0
  - commonmark=0.9.1=pyhd3eb1b0_0
  - coverage=6.3.2=py37h7f8727e_0
  - cryptography=39.0.1=py37h9ce1e76_0
  - cycler=0.11.0=pyhd3eb1b0_0
  - cyrus-sasl=2.1.28=h9c0eb46_1
  - dbus=1.13.18=hb2f20db_0
  - debugpy=1.5.1=py37h295c915_0
  - decorator=5.1.1=pyhd3eb1b0_0
  - defusedxml=0.7.1=pyhd3eb1b0_0
  - dill=0.3.6=py37h06a4308_0
  - distlib=0.3.6=py37h06a4308_0
  - docutils=0.18.1=py37h06a4308_3
  - entrypoints=0.4=py37h06a4308_0
  - execnet=1.9.0=pyhd3eb1b0_0
  - expat=2.6.4=h6a678d5_0
  - filelock=3.9.0=py37h06a4308_0
  - flake8=4.0.1=pyhd3eb1b0_1
  - flit-core=3.6.0=pyhd3eb1b0_0
  - fontconfig=2.14.1=h52c9d5c_1
  - fonttools=4.25.0=pyhd3eb1b0_0
  - freetype=2.12.1=h4a9f257_0
  - future=0.18.3=py37h06a4308_0
  - giflib=5.2.2=h5eee18b_0
  - glib=2.78.4=h6a678d5_0
  - glib-tools=2.78.4=h6a678d5_0
  - gst-plugins-base=1.14.1=h6a678d5_1
  - gstreamer=1.14.1=h5eee18b_1
  - icu=58.2=he6710b0_3
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prefix: /opt/conda/envs/jupytext

tests/test_read_simple_percent.py::test_cell_marker_has_same_indentation_as_code
tests/test_read_simple_percent.py::test_multiple_empty_cells tests/test_read_simple_percent.py::test_cell_markers_option_in_contents_manager tests/test_read_simple_percent.py::test_default_cell_markers_in_contents_manager tests/test_read_simple_percent.py::test_default_cell_markers_in_contents_manager_does_not_impact_light_format
tests/test_read_simple_percent.py::test_read_simple_file tests/test_read_simple_percent.py::test_read_cell_with_metadata tests/test_read_simple_percent.py::test_read_nbconvert_script tests/test_read_simple_percent.py::test_read_remove_blank_lines tests/test_read_simple_percent.py::test_no_crash_on_square_bracket tests/test_read_simple_percent.py::test_nbconvert_cell tests/test_read_simple_percent.py::test_nbformat_v3_nbpy_cell tests/test_read_simple_percent.py::test_first_cell_markdown_191 tests/test_read_simple_percent.py::test_multiline_comments_in_markdown_1 tests/test_read_simple_percent.py::test_multiline_comments_in_markdown_2 tests/test_read_simple_percent.py::test_multiline_comments_format_option tests/test_read_simple_percent.py::test_multiline_comments_in_raw_cell tests/test_read_simple_percent.py::test_multiline_comments_in_markdown_cell_no_line_return tests/test_read_simple_percent.py::test_multiline_comments_in_markdown_cell_is_robust_to_additional_cell_marker tests/test_read_simple_percent.py::test_single_triple_quote_works tests/test_read_simple_percent.py::test_docstring_with_quadruple_quote
jupytext/version.py jupytext/cell_reader.py CHANGELOG.md jupytext/cell_to_text.py
jupytext/version.py jupytext/cell_reader.py CHANGELOG.md jupytext/cell_to_text.py