Arthropod ectoparasites generally have nutrient-poor diets and are dependent on their bacterial symbionts for nutrient acquisition, development, and immune response initiation. As the body of research on parasite-microbiome interactions continues to grow, it is becoming more apparent that the parasite is not an island that physically and biologically constrains the microbiome. Suitable habitat fragment size, isolation, and distance from a source are important variables influencing community composition of plants and animals, but the role of the environment in determining composition and variation of host-associated microbial communities is poorly known. It is hypothesized that evolution and ecology of an arthropod parasite will influence its microbiome more than broader environmental factors, but this hypothesis has not yet been tested. To compare the relative influence of the broader environment to that of phylogenetic constraint on the microbiome, we applied high-throughput sequencing of the V4 region of 16S rRNA from 222 obligate ectoparasitic bat flies (Streblidae and Nycteribiidae) collected from 155 bats (representing six species) from ten habitat fragments in the Atlantic Forest of Brazil. We find that parasite species identity is the strongest driver of microbiome composition. To a lesser extent, reduction in habitat fragment area is associated with a reduction in connectance of microbial interaction networks and an increase in modularity, but size-independent measures of network topology and bacterial taxon richness do not show an impact of the environment. Instead, habitat fragments that support more diverse bat and bat fly communities also support more connected bacterial interaction networks.