Adult stem/progenitor cells (PC) have been studied vigorously over the past years in their basic cell and molecular biology, association with disease development and potential therapeutics. Corneal and retinal PCs are the two major adult stem cell populations in the eye. Corneal epithelial progenitor cells (CEPCs) residing in limbal basal region play an active role in corneal surface wound healing. They are stimulated to proliferate and differentiate to surface epithelial cells. Much is to be understood on the regulatory factors and mechanisms of the differentiating processes. There is also a need in identifying definitive biological markers for ready isolation of these cells for further studies. Our group has been working on CEPC biology, cell isolation and epigenetics. In our earlier studies, we found nuclear matrix degradation in long-term culture of CEPCs. In exploring novel and effective method of CEPC identification, we used fluorescence-activated cell sorting to characterize cells obtained from human cornea rims. We found that quiescent cells with the feature of connexin43^-/ABCG2^high/Notch1^high are able to form holoclones in culture. Subsequent proteomic analysis has given information of putative molecular markers unique to CEPCs. We also investigate the role of microRNA in the regulation of CEPC activities and recently confirm that microRNA-145 is enriched in human limbal epithelium and regulates corneal epithelial differentiation, probably via its targeting on cell surface integrin b8. Human CEPCs overexpressing microRNA-145 show up-regulated expression of corneal differentiation markers, cytokeratin 3/12 and connexin-43, and generates a defective epithelium in vitro.