Abstract The Neotropical bat species Artibeus planirostris and Eptesicus furinalis present a different morphology of the female reproductive organs: the first presents a simplex uterus, while the second presents a bicornuate uterus, but there is no information about their ovaries. Our aim was to compare the general ovary morphology and the folliculogenesis process in these species to increase the knowledge about the reproductive diversity of tropical bats. We observed a morphological distinction between the ovaries of both species: A. planirostris presents the primordial follicles located in a cranial portion of the ovary and the interstitial gland cells are not distinctive, while in E. furinalis, the primordial follicles are located throughout the cortex, and there is an abundance of interstitial gland cells. Both species present binovular or triovular follicles. Artibeus planirostris is a monovular species, with a preferential ovulation in the left side. Some females of E. furinalis exhibited two corpora lutea in the same ovary, and others presented a corpus luteum in both right and left ovaries at the same time; thus, E. furinalis is a polyovular species. Our results express the variation between two Neotropical species, reflecting the great variation in the reproductive aspects in Chiroptera.