After the Hayden Survey was absorbed into the U.S. Geological Survey in 1879, Holmes went to Munich, Germany, to further his art studies under Frank Duveneck and to take lessons in museum making from Adolphe B. Meyer of Dresden's Anthropology Museum. On Holmes's return to the U.S., he was hired by the Geological Survey and assigned to Clarence Dutton as a geologist and illustrator. Holmes illustrated the atlas for Dutton's Tertiary History of the Grand Canyon District (1882); his triptych panorama of the Grand Canyon from Point Sublime is a masterpiece of American scientific illustration. He was also a noted mountain climber, and a peak in Yellowstone National Park — Mount Holmes — was named in his honor. In 1875, Holmes began studying the remains of the Ancestral Pueblo culture in the San Juan River region of Utah. His models of ancient Indian ruins were a sensation at the Centennial International Exhibition in Philadelphia. Holmes became particularly interested in prehistoric pottery and shell art, producing the published works of Art in Shell of the American Indians (1883) and Pottery of the Ancient Pueblos (1886). He expanded these studies to include textiles, and he became well known as an expert in both ancient and existing arts produced by Native Americans of the Southwest. In 1889 he discovered and reported Indian petroglyphs in central West Virginia.