To investigate the molecular markers of corneal epithelial stem cells. The anatomy structure of corneal limbus was analyzed by histological examination. Fluorescence microscopy and laser scan confocal microscopy (LSCM) were used to evaluate the expression of un differentiation markers as p63, ABCG2, alpha6, alpha9 and beta1 integrin, alpha-enolase, EGFR, cytokeratin 19 (CK19) and CD71 in cornea-limbus sections and whole mount cornea tissue using immunohistochemistry staining. Semiquantitative RT-PCR and in situ hybridization (ISH) were used to evaluate gene expression of corneal and limbal epithelia. The limbal area in horizontal cut direction showed that limbal epithelial cells were as papilloma-form to correspond to the Palisades of Vogt environment. The expressions of beta1 integrin, K19, alpha-enolase and EGFR were much stronger in limbal basal cells than superficial cells. Un differentiation markers p63, ABCG2, alpha9 integrin were detected only in the basal limbal epithelial cells. LSCM and RT-PCR results showed that the protein and mRNA of p63, ABCG2 and alpha9 integrin were only detected in limbal epithelia. ISH showed that p63 mRNA only expressed in the limbal basal epithelial layer. The corneal limbal epithelial area is papilloma-form. Limbal stem cells have complex markers as p63 expressing in the nuclei, ABCG2 in the cytoplasm and alpha9 integrin expressing in the membrane. With these markers complex, it is easy to distinguish limbal stem cells from other epithelial cells in cornea.