Plethodontid salamanders are generally considered resistant to fungal pathogens due to their symbiotic relationships with skin bacteria. We hypothesized that microhabitat selection among salamander species can affect bacterial recruitment, leading to differences in microbial community and resistance against pathogens. In this study, we compared skin bacteria isolated from three closely related species with different microhabitat preferences: Plethodon cinereus, a habitat generalist, and two microendemic species, Plethodon sherando and Plethodon hubrichti. To do this, we swabbed the skin of the salamanders (N= 9 per species) and isolated distinct colonies of bacteria. We then sequenced the 16S ribosomal gene and identified bacteria to the highest taxonomic level possible. To test their inhibition ability, we challenged bacterial isolates against Batrachochytrium dendrobatidis, a widespread amphibian fungal pathogen. In addition, we collected publicly available microbiome datasets and investigated the occurrence and overlap of isolated bacteria with amplicon sequence variants detected via targeted sequencing. This information is expected to provide a broader context of the microbial diversity found in our focal species compared with other Plethodontid family members. Our results showed differences in bacterial composition where P. cinereus had the lowest diversity yet the highest number of antifungal bacteria. Our findings indicate these three salamanders encounter distinct bacterial species pools and that high diversity of bacteria does not necessarily correlate with a high richness of antifungal bacteria. Considering a species microhabitat can widen our perspective about how microbiome diversity of amphibians leads to a more equipped fight against fungal threats.