The ability to reproduce in captivity is an essential component of lion tamarin (Leontopithecus) conservation programs. However, infections such as vaginitis, cervicitis, and endometritis are important diseases that may influence the reproduction of these animals. Therefore, it is important to detect continuous or occasional vaginal microbial populations, and to understand their potential role as an endogenous source of infection [Collins, 1964; Blue, 1983; Pugh et al., 1986]. Vaginal swabs were collected from 25 female tamarins of the three currently available species (L. rosalia, L. chrysopygus, and L. chrysomelas) at the Center of Primatology in Rio de Janeiro, Brazil. The swabs were processed according to standard mycological protocols, and isolates were biochemically characterized. Fungal isolates were recovered from 16 animals (64.0%). The results showed that 70.6% of the isolated microorganisms consisted of yeast, including three species of Candida (mainly C. glabrata). We suggest that this species is a resident member of the normal vaginal flora in Leontopithecus. Filamentous fungi (mainly from Trichosporon, Aspergillus, and Penicilliumgenera) constituted 29.4% of the isolates, and were considered to be transitory contaminants of the genital area. We suggest that colonization of the vaginal environment is related to the endocrine pattern associated with the reproductive status of these animals, but not to parity.