The cornea lines the anterior ocular surface and is necessary to control and focus incoming light toward the retina. The topmost layer of the cornea consists of a stratified epithelium that is essential for maintaining corneal transparency and visual acuity. This layer acts as a protective barrier, and as such, is subject to frequent injuries and environmental insults. Given the importance of the corneal epithelium, long-term maintenance is critical and is sustained by a population of stem cells that exist within the periphery of the tissue in an area known as the limbus. While the existence of these stem cells is well established, their behaviors in vivo and their regulation are poorly understood. To address these gaps in knowledge, we developed an intravital imaging technique that uses two-photon microscopy to visualize cellular activity in real time in the eyes of live mice. Using this method, in conjunction with various genetic mouse models, we captured and analyzed the activity and regulation of stem cells in the limbus by live imaging. We found that the stem cells in the limbus are heterogenous and can be divided into two populations. One in the inner limbus that gives rise to transient progenitors that exit the niche and move centripetally to maintain the corneal tissue. And the other in the outer limbus that gives rise to progenitors that display only local clonal dynamics during homeostasis, but can contribute to corneal regeneration after injury. Additionally, we observed changes in the cycling dynamics of the basal epithelial cells after denervation, which points to corneal nerves being an important component of the niche. Together, this work provides novel insights into the mechanisms underlying stem cell behavior and regulation in the corneal epithelium.