Previous field studies suggested that Eonycteris spelaea reproduces at all times of the year, with peak periods that may be associated with the rainy seasons. This study reports the anatomical and histological features that are associated with this pattern, using specimens obtained from this study. Our data confirm that this species is indeed aseasonal and polyestrous, and that females are monotocous and appear to undergo two pregnancies a year. The gross morphology of the male and female reproductive tracts is described. Adult males were found to have spermatogenic testes and secretory accessory sex glands year around. Adult females also were reproductively active year around. Individuals were pregnant, lactating or pregnant and lactating at each sampling. Both sexes possess specialized para-anal sebaceous glandular organs whose odoriferous secretions may have a role as secondary pheromones in the reproductive behavior of Eonycteris.