Growing evidences show that the pathogenesis of majority human diseases is influenced by the abnormalities of epigenetic and genetic mechanism. The major epigenetic factors such as DNA methylation, histone modifications, and microRNA (miRNA) interact with each other to regulate gene expression and determine cell phenotype.Epigenetics is currently become a hot topic of biomedical research, which focus on how whole genome is regulated by epigenetics mechanism and its roles in life development, senescence, regeneration, tumorgenesis and the pathogenesis of complex disease. The occurrence of variety of eye diseases may be mediated through the interaction of environmental and genetic factors which in turn regulated by epigenetic mechanisms.Emphasizing the epigenetic research in eye may provide a new insight of the understanding of pathogenesis of complex eye disease and a novel approach of its treatment.