Bioinformatics, an emerging discipline focusing on genomics and proteomics, is both comprehensive and interdisciplinary of biology, computer science, information engineering and statistics. In the ophthalmic biological genetic research, cornea, lens, aqueous humor, vitreous and retina are ideal bioinformatic research objects in the field of ophthalmic biological genes because of their abundance in biological information. Genomics testing techniques have the characteristics of high efficiency and accuracy, which helps us to screen the differentially expressed genes related to ophthalmic tumors and genetic diseases; Proteomics can help us analyze the protein expression profile and functional changes caused by the high and low gene expression in intraocular fluid or isolated cells in diseases states, revealing the mechanism of disease. This paper mainly summarizes the application of bioinformatics in ophthalmic diseases, and preliminarily envisage its impact on the current treatment, the existing problems and the development trend in the future.