Molecular epidemiology is a new branch of eye epidemiology that combines theories and methods in both epidemiology and molecular biology. The definition of molecular epidemiology is to use biological and, in particular, genetic markers (nucleic acid, protein) as measures for detecting the propensity of a disease developing, or as an indicator of a disease or an exposure in the studies of disease distribution. Molecular epidemiology has the same objectives as conventional ophthalmic epidemiology in a defined population. The main designs used in ophthalmic molecular epidemiology include descriptive study, case control study, and nested case control study. Currently, molecular experimental techniques mainly include single nucleotide polymorphism, ELISA, protein and mRNA array, microRNA and the study of epigenetic markers. Gene susceptibility biomarker is one of the most commonly used molecular markers. The findings of ophthalmic molecular epidemiology studies can be used to design personalized therapy. Undoubtedly, ophthalmic molecular epidemiology will evolve and develop in the new era for the prevention and control of complex eye diseases such as age-related macular degeneration, cataract, glaucoma and diabetic retinopathy.