All animals and plants have intimate associations with microbes. Opinion has shifted from viewing microbes primarily as pathogens to the idea that healthy animals and plants carry specialized communities of coevolving microorganisms. However, the generality of this proposition is unknown because surveys rarely compare host-associated microbes with samples from relevant microhabitats. Symbiotic communities might be assembled from local environments with little evolutionary specialization. We evaluated the specificity of bacteria associated with salamander skin in comparison with surfaces in their immediate environments using 16S rRNA sequences. Host-associated and free-living samples were significantly different. However, relative abundances were strongly correlated; the most abundant taxa on salamander skin were also most abundant on moist debris on the forest floor. Thus, although bacterial assemblages on salamander skin are statistically differentiated from those on inanimate surfaces, they are not entirely ‘distinct’. Candidate salamander specialists were few in number and occurred at low relative abundances. Within some OTUs, differences in allele frequency suggested genetic specialization at finer levels. Although host-associated and free-living assemblages were similar, a range of more or less specialized symbiotes was evident and bacteria on salamander skin were often specific genotypes of OTUs commonly found on other moist surfaces in the environment.