Seabird ticks are known reservoirs of bacterial pathogens of medical importance, however, ticks parasitizing tropical seabirds have received less attention than their counterparts from temperate and sub-polar regions. Recently, Rickettsia africae was described to infect seabird ticks of the western Indian Ocean and New Caledonia, constituting the only available data on bacterial pathogens associated with tropical seabird tick species. Here, we combine a pyrosequencing-based approach with a classical molecular analysis targeting bacteria of potential medical importance in order to describe the bacterial community in two tropical seabird ticks, Amblyomma loculosum and Carios (Ornithodoros) capensis. We also investigate patterns of prevalence and host specificity, within the biogeographical context of the western Indian Ocean Islands. The bacterial community of the two tick species was characterized by high dominance of Coxiella and Rickettsia. Our data support a strict Coxiella-host tick specificity, a pattern resembling the one found for Rickettsia spp. in the same two seabird tick species. Both high prevalence and stringent host tick specificity suggest that these bacteria may be tick symbionts with probable vertical transmission. Detailed studies of the pathogenicity of these bacteria will now be required to determine whether horizontal transmission can occur and to clarify their status as potential human pathogens. More generally, our results show that the combination of Next Generation Sequencing with targeted detection/genotyping approaches proves efficient in poorly investigated fields where research can be considered as starting from scratch.