Mammalian corneal development is a multistep process, including formation of corneal epithelium (CE), endothelium and stroma during embryogenesis followed by postnatal stratification of the epithelial layers, and continuous renewal of the epithelium to replace the most outer corneal cells. Herein we employed Cre-loxP system to conditionally deplete Pax6 proteins in two domains of ocular cells, including the ocular surface epithelium (cornea, limbus and conjunctiva) or postnatal CE, via K14-cre or Aldh3-cre, respectively. Earlier and broader inactivation of Pax6 in the OSE resulted in thickened OSE with CE and limbal cells adopting the conjunctival keratin expression pattern. More restricted depletion of Pax6 in postnatal CE resulted in the abnormal cornea marked by reduced epithelial thickness despite of increased epithelial cell proliferation. Immunofluorescence studies showed loss of Keratin 12, an intermediate filament and diffused expression of adherens junction components, together with reduced tight junction protein, Zonula occludens-1 (ZO-1). Furthermore, expression of Keratin 14, basal cell marker in apical layers, indicates impaired differentiation of corneal epithelial cells. Collectively, our data demonstrate that Pax6 is essential for maintaining proper differentiation and strong intercellular adhesion in postnatal corneal epithelial cells, whereas limbal Pax6 is required for preventing the outgrowth of conjunctival cells to the cornea.