Male and female plethodontid salamanders have specialized cloacal glands associated with the reproductive activity. The reproductive cycle in Bolitoglossa nicefori is characterized by males that are potentially reproductive throughout the year, and females that are reproductive only for a few months. To determine whether morphological and histochemical variation occur in cloacal structures related to reproductive activity, the cloacal region of male and female specimens of B. nicefori was studied in different stages of their annual reproductive cycle using light microscopy and compared with features reported in other plethodontid salamanders. The main anatomy and histology of the male and female cloacal regions of B. nicefori are similar to those of other salamanders; however, in comparison to other Bolitoglossa previously studied, B. nicefori has a relatively larger cloacal tube and a tubular rather than acinar spermatheca. As a common trait, the spermatheca has a common tube that diverges into two tubules, before branching into spermathecal tubules, horizontally arranged on frontal planes. The secretions of the spermathecal glands differed between reproductive and nonreproductive adult females. This secretory product consists of prevailing neutral carbohydrates that were related to the increase in ovarian follicular size during the breeding season. Sperm was found only in the spermatheca of reproductive periovulatory females, suggesting that the reproductive cycle involves a no long-term storage of sperm. Although males can produce sperm throughout the year, spermatophores, namely specialized structures involved in sperm transport, were found in their cloaca only during the breeding season. In these males, some of the cloaca-associated glands were seen to undergo change their secretory activity and their secretory products were related to spermatophore formation.