Parasitic arthropods often depend on symbiotic microbes to supplement their narrow diets. Facultative parasites exhibit variation in their parasitic activity and diet, and thus, might be expected to have greater variation in their microbial communities. Further, individuals that engage in more parasitic activity may have different microbial communities from those less parasitic within the same population, but this remains unexplored. Here, we compared the microbial communities of individuals exhibiting parasitic (n = 30) and nonparasitic (n = 29) tendencies from two populations (one originating from Tampa, FL and the other Gainesville, FL) of facultatively ectoparasitic mites (Macrocheles muscaedomesticae). Microbial alpha diversity was similar across mites, regardless of parasitic activity or population. Using ANOSIM, we found that our dataset clustered into four groups. The composition of microbial communities of non-parasitic M. muscaedomesticae mites originating from Tampa and Gainesville was distinct from each other, whereas the parasitic mites had a much greater degree of overlap. We hypothesize that the association of parasitic individuals with fly hosts drove the observed overlap in their microbial communities.