creating and theming register form in drupal 7
You can try this one

To implement hook_form_alter() in a module and set the form's #theme property:

    function mymodule_form_user_register_form_alter(&amp;$form, &amp;$form_state, $form_id) {
      $form['#theme'] = 'user_register';
    }


and add this code to template.php

    function mytheme_theme($existing, $type, $theme, $path){
      return array(
        'user_register' =&gt; array(
          'render element' =&gt; 'form',
          'template' =&gt; 'templates/user-register',
        ),
      );
    }

function mytheme_preprocess_user_register(&amp;$variables) {
  $variables['rendered'] = drupal_render_children($variables['form']);
}


Also, create a user-register.tpl.php in 


  sites/all/modules/YOUR_module/templates/user-register.tpl.php


to add the 'markup' for the desired output and

&lt;?php echo $rendered; ?&gt; 


to print the form.

For more information, follow this https://www.drupal.org/node/1211520 

Hope, it works.