Abstract: The present disclosure describes novel methods for localized and controlled staining of intact corneal tissue surfaces to provide therapeutic benefits in ophthalmic applications, such as for example, the correction of iris defects, the correction of corneal tissue scarring, and the creation of a pupil in aniridia. A first method for staining tissue surfaces is directed to covalently bonding sulfonic acid dyes to deprotonated proteins in tissue. Another disclosed method is directed to staining corneal tissue surfaces with black sulfonic acid dye compositions, particularly for forming black rings on the corneal surface.