Prostate cancer is consistently the most frequently diagnosed cancer in American males as well as the second leading cause of cancer-related mortality. This underscores the dire need to understand the healthy prostate and how it can transform into a diseased state. Therefore, I have sought to investigate the heterogeneity and ontogeny of the mouse and human prostate. To do this, I employed single-cell RNA-sequencing, electron microscopy, immunofluorescence, and immunohistochemical analyses to identify specific cell populations, as well as lineage tracing, organoid culture, and tissue recombination assays to assess the function and origin of these populations. I discovered a profound level of heterogeneity uniquely within the luminal epithelial compartment of the prostate, including several novel populations. These luminal populations differ in distribution between mouse prostate lobes and along the proximal-distal axis within each lobe. These populations demonstrated significant differences in progenitor behavior in both organoid culture and tissue recombination assays, as shown by their differential abilities to proliferate, generate patterned structures, and differentiate into distinct cell types. Comparisons of the mouse prostate cell populations to cells from several benign human prostate samples showed that there is also luminal heterogeneity in the human prostate, and that several mouse populations have substantial gene expression overlap with human prostate populations. The observed luminal heterogeneity as well as the functional differences were consistent across several different published studies of the mouse prostate, and cross-species transcriptional similarities between populations were maintained across additional human samples, indicating that these findings are robust. My findings suggest that the luminal compartment of the mouse prostate contains distinct populations of cells that may act as reserve progenitors, and that their distribution across the prostate lobes could be functional. Additionally, if these populations can be cells of origin for prostate cancer, then their differences in progenitor behavior could contribute to the heterogeneity observed in prostate cancer prognosis and treatment response, which could have substantial clinical implications for patients.