Adult tissues contain label-retaining cell (LRC)s, which are relatively slow-cycling and considered to represent a unique property of tissue stem cell (SC)s. In the ocular surface epithelium, LRCs are detected in the limbus, a boundary between cornea and conjunctiva, and the fornix of the conjunctiva; however, the character of LRCs and identity of SCs remain unclear due to lack of appropriate molecular markers. Here we show that the ocular surface epithelium accommodates spatially distinct stem/progenitor populations with different cell division frequency. By combining EdU pulse-chase analysis and lineage tracing with three CreER transgenic mouse lines: Slc1a3 CreER , Dlx1 CreER and K14 CreER , we detect distinct dynamics of epithelial SCs in the cornea and conjunctiva. In the limbus, long-lived SCs are labeled with Slc1a3 CreER and they either migrate centripetally toward the central cornea or laterally expand their clones within the limbal region. In the central cornea, cells are mostly non-LRCs, labeled by Dlx1 CreER and K14 CreER , and the number of clones declines after a short period of time with rare long-lasting clones, suggesting their properties as short-lived progenitor cells. In the conjunctival epithelium, which consists of bulbar, fornix and palpebral conjunctiva, each territory is regenerated by compartmentalized, distinct SC populations without migrating one region to another. The severe damage of the cornea leads to the cancellation of SC compartments, causing conjunctivalization of the eye, whereas milder limbal injury induces a rapid increase of laterally-expanding clones in the limbus. Taken together, our work provides lineage tracing tools of the eye and defines compartmentalized, multiple SC/progenitor populations in homeostasis and their behavioral changes in response to injury.