Experiments conducted on captive animals allow scientists to control many variables; however, these settings are highly unnatural. Previous research has documented a large difference in microbial communities between wild animals and captive-bred individuals. However, wild-caught animals brought into captivity might retain their natural microbiota and thus provide a better study system in which to investigate the ecology of the gut microbiome. We collected individuals of the desert woodrat (Neotoma lepida) from nature and investigated changes in the microbial community over 6 months in captivity. Additionally, we inventoried potential environmental sources of microbes (food, bedding) from the wild and captivity. We found that environmental sources do not make large contributions to the woodrat gut microbial community. We documented a slight decrease in several biodiversity metrics over 6 months in captivity, yet the magnitude of change was small compared with other studies. Wild and captive animals shared 64% of their microbial species, almost twice that observed in other studies of wild and captive-bred individuals (≤ 37% shared). We conclude that wild-caught animals brought into captivity retain a substantial proportion of their natural microbiota and represent an acceptable system in which to study the gut microbiome.