Animal-associated microbiota is expected to impose crucial effects on the host's fitness-related performance, including reproduction. Most research to date has focused on interactions between the host with its gut microbiota; however, there remain considerable gaps in knowledge regarding microbial consortia in other organs, including interspecific divergence, temporal stability, variation drivers, and their effects on the host. To fill these gaps, we examined oral and vaginal microbiota composition in four free-living mouse species of the genus Apodemus, each varying in the degree of female promiscuity. To assess temporal stability and microbiota resistance to environmental change, we exposed one of the species, Apodemus uralensis, to standardized captive conditions and analyzed longitudinal changes in its microbiota structure. Our results revealed the existence of a "core" oral microbiota that was not only shared among all four species but also persisted almost unchanged in captivity. On the other hand, vaginal microbiota appears to be more plastic in captive conditions and less species-specific in comparison with oral microbiota. This study is amongst the first to describe oral microbiota dynamics. Furthermore, the vaginal microbiota results are especially surprising in light of the well-known role of stable vaginal microbiota as a defense against pathogens. The results indicate the existence of diverse mechanisms that shape each microbiota. On the other hand, our data provides somewhat ambiguous support for the systematic effect of phylogeny and social system on both oral and vaginal microbiota structures. Symbiotic microbiota have adapted to the diverse conditions found within animal bodies and have a profound effect on many aspects of an individual's life, including its health 1 and fitness 2,3. Species-specific microbiota alter the body's odor 4 , protect its host against pathogens 5,6 , and influence mating preferences 7 or behavior in general 8. However, most research to date has focused on gut microbiota 7,9,10 ; thus, most body parts remain unexplored in non-human hosts. For example, skin microbiota 6 or vaginal microbiota 11 also contribute to the host's health and fitness and it has been shown that tissue-specific differences exist in the expression of antimicrobial proteins, which presumably regulate the abundance and diversity of microbiota along the eyes-nose-oral cavity-gut axis 12-14. As such, the detection of particular factors that shape microbial composition in particular tissues is challenging. Variation in microbiota between geographically distinct, but ecologically comparable, populations of the same species suggests that local environmental pools are important sources for host-associated microbiota 15. Especially the diet seems to be crucial for the gut microbiota composition. The standardized diet in captivity not only alters the microbiota but also hinders the microbiota recovery after releasing back into the natural environment 16. At the same time, however, environmental microbiota dif...