Gut microbes can largely influence the ecology and evolution of mammalian hosts. As research in this area increases, it will be necessary to collect fecal samples from nature to inventory microbial populations. Here, we tested the appropriateness of using feces collected from live-traps for microbiome studies. We found that feces collected from the traps containing the desert woodrat (Neotoma lepida) did not differ from aseptically collected feces in terms of microbial community structure, abundances of bacterial phyla, or measurements of α-diversity. Roughly 83% of the microbes in trap-collected feces represented the endogenous microbiota. Thus, we suggest that feces collected from small mammal traps are acceptable for studying the microbiota of wild, small mammals.