In rodents, progesterone receptors PRA and PRB have different and often non-overlapping roles, and this study asked whether different activities of the PR proteins in mouse are related to differences in their expression in reproductive tissues. The individual expression of PRA and PRB was determined immunohistochemically in mammary gland and uterus, during the estrous cycle or in response to endocrine manipulation. In the mammary gland, PRA and PRB were co-located in PR+ epithelial cells, with little change during the estrous cycle. In the uterus, PRA was not detected in luminal epithelium at any stage of the cycle and PR+ luminal cells expressed only PRB. In the stroma and myometrium PRA and PRB levels fluctuated with cyclical systemic hormone exposure. Observation of functional endpoints suggested that augmented stromal and/or myometrial PRA in proestrus inhibited ER expression and epithelial proliferation. Co-location of PRA and PRB was hormonally regulated, and ovariectomy did not reproduce the expression of PRA and PRB in the uterus during the estrous cycle. While PRB was the only PR in the luminal epithelium in cycling mice, ovariectomy restored PRA expression resulting in PRA:PRB co-location. In stroma and myometrium PRA and PRB co-located in PR+ cells, but ovariectomy reduced PRA levels more than PRB resulting in PRB-only expressing cells. This study has shown that non-overlapping PRA and PRB expression in the uterus, in particular the lack of PRA, and expression of PRB-only in the luminal epithelium throughout the estrous cycle, is likely to contribute to the distinct roles of PRA and PRB in the adult mouse.