Simple Summary Multi-oocyte follicles have been reported in several mammals, especially in rabbits and hamsters, although their significance remains unclear. The present study compared ovarian histology, focusing on folliculogenesis, between two inbred cotton rat strains maintained at Hokkaido Institute of Public Health and the University of Miyazaki. Abundant multi-oocyte follicles and double-nucleated oocytes were observed in the Hokkaido strain, whereas Miyazaki had fewer multi-oocyte follicles and lacked double-nucleated oocytes. These findings indicate that early folliculogenesis events such as oocyte nest breakdown and oocyte vitality, rather than proliferation and cell death in each oocyte, affect the unique ovarian phenotypes found in cotton rats, including multi-oocyte follicles or double-nucleated oocytes, and their differences between strains. Therefore, these results can clarify mammalian folliculogenesis and its abnormal processes. Most mammalian ovarian follicles contain only a single oocyte having a single nucleus. However, two or more oocytes and nuclei are observed within one follicle and one oocyte, respectively, in several species, including cotton rat (CR, Sigmodon hispidus). The present study compared ovarian histology, focusing on folliculogenesis, between two inbred CR strains, HIS/Hiph and HIS/Mz. At 4 weeks of age, ovarian sections from both the strains were analyzed histologically. Multi-oocyte follicles (MOFs) and double-nucleated oocytes (DNOs) were observed in all stages of developing follicles in HIS/Hiph, whereas HIS/Mz had MOFs up to secondary stages and lacked DNOs. The estimated total follicles in HIS/Mz were almost half that of HIS/Hiph, but interstitial cells were well developed in HIS/Mz. Furthermore, immunostaining revealed no clear strain differences in the appearance of oocytes positive for Ki67, PCNA, and p63 in MOF or DNOs; no cell death was observed in these oocytes. Ultrastructural analysis revealed more abundant mitochondrial clouds in oocytes of HIS/Hiph than HIS/Mz. Thus, we clarified the strain differences in the CR ovary. These findings indicate that early events during folliculogenesis affect the unique ovarian phenotypes found in CRs, including MOFs or DNOs, and their strain differences.