Microbial communities play central roles in animal health. Host species, environmental conditions and presence of pathogens can affect the diversity and composition of animal-associated microbiomes. Amphibians form integral and functionally important symbioses with microbes. The amphibian microbiome interacts with pathogens, and can protect hosts from disease, including the disease chytridiomycosis, caused by skin infection by Batrachochytrium dendrobatidis (Bd). The implications of amphibian-microbiome associations are difficult to predict because little is known about the factors shaping bacterial communities or their functional traits, such as anti-Bd properties. I used culture-dependent and culture-independent methods to characterize the skin microbiome of Plethodon salamanders in field and laboratory studies. I hypothesized that the evolutionary history, environmental conditions, and health status of the hosts shape skin bacterial community assemblages. In a field study, I sampled sympatric, congeneric salamander species (Plethodon cinereus, P. glutinosus, P. cylindraceus) across three localities to quantify the distribution of both anti-Bd bacteria and the entire bacterial community. I identified 50 anti-Bd bacterial OTUs and 480 bacterial OTUs overall on the salamander skin, with high prevalence and abundance of anti-Bd bacterial genera Pseudomonas, Acinetobacter and Stenotrophomonas. Within a locality, co-occurring salamanders generally had similar microbiome diversity and composition patterns, but these differed among sites. This indicates that environment is more influential in shaping skin microbiome patterns than differences in host properties in these species. I sampled P. cinereus along an elevational gradient, as a proxy for environmental variables that co-vary with elevation. Microbiome diversity and composition changed with elevation, in which compositional changes were related to soil pH. In a laboratory experiment, I quantified the responses of P. cinereus and the skin microbiome to temperature (13, 17, 21 °C) and pathogen (Bd+, Bd-) exposure to determine whether the native microbiome affected survival at natural temperatures. Temperature changed the microbiome, but this did not prevent host mortality from Bd. Instead, Bd exposure changed the microbiome and caused 78% mortality. My results demonstrate that environmental conditions and pathogen presence are important factors determining skin microbiome structure in Plethodon salamanders. These findings contribute to our understanding of animal-microbial symbioses, microbial community ecology, and amphibian disease ecology.