The corneal epithelium is continuously being renewed. Differentiated epithelial cells originate from limbal stem cells (LSCs) located in the periphery of the cornea, the corneoscleral limbus. We have recently identified superoxide dismutase 2 (SOD2) and cytokeratin (CK) 15 as limbal basal cell markers and potential markers for LSCs and early transient amplifying cells in human adults. In this study, we describe the development of the ectodermally derived LSCs and the mesodermally derived niche cells from the time at which the cornea is defined (week 6) until the formation of the early limbal niche (week 14) in human embryos and fetuses. The expression of SOD2 and CK15 was investigated together with other recently identified limbal proteins. Previously suggested LSC and differentiation markers (PAX6, aquaporin-1 and nestin) were also investigated. Both SOD2 and CK15 were present in the corneal epithelium from week 6. However, in week 14 they were predominantly expressed in the limbal epithelium. Both proteins were expressed already from week 7 in a stromal triangular region from which the early mesodermal limbal niche most likely originates. PAX6 was expressed in both ectodermally and mesodermally derived parts of the limbal niche, underscoring the importance of PAX6 in niche formation.