The Nycteribiidae are obligate blood-sucking Diptera (Hippoboscoidea) parasitizing bats. Depending on species, these wingless flies exhibit either high specialism or generalism towards their hosts, which may in turn have important consequences in terms of their associated microbial community structure. Bats have been hypothesized to be reservoirs of numerous infectious agents, some of which have recently emerged in human populations. Thus, bat flies may be important in the epidemiology and transmission of some of these bat-borne infectious diseases, acting either directly as arthropod vectors or indirectly by shaping pathogen communities among bats populations. In addition, bat flies commonly have associations with heritable bacterial endosymbionts that inhabit insect cells and depend on maternal transmission, through egg cytoplasm, to ensure their transmission. Some of these heritable bacteria are likely obligate mutualists required to support bat fly development but others are facultative symbionts with unknown effects. Here, we present bacterial community profiles obtained from seven bat fly species, representing five genera, parasitizing bats from the Malagasy region. The observed bacterial diversity includes Rickettsia, Wolbachia, several Arsenophonus-like-organisms, as well as other members of the Enterobacteriales, and a widespread association of Bartonella bacteria from bat flies of all five genera. Using the well-described host specificity of these flies and data on community structure from selected bacterial taxa with either vertical or horizontal transmission, we show that host/vector specificity and transmission mode are both important drivers of bacterial community structure.