In the current context of global change and intensification of coral bleaching events, it is critical to better understand the functioning of the coral holobiont. This begins with separating the effects of genetics and environment on assembly of its bacterium and Symbiodiniaceae communities. Using metabarcoding analyses, we analyzed 53 colonies from three Millepora fire coral species across four Indo-Pacific locations: Mayotte, Rodrigues, Papua New Guinea and Moorea. A core microbiome of 13 bacterial OTUs was present in all species and across the Indo-Pacific region. While Proteobacteria were the dominant bacterial phylum, Spirochaetes, Bacteroidetes, and Tenericutes were also present. Symbiodiniaceae communities were dominated by the Symbiodinium and Cladocopium genera. While species host was the main driver of bacterial species richness, geographic location shaped Symbiodiniaceae species richness. Overall, distinct mechanisms seem to shape the bacterial and Symbiodiniaceae communities present in fire corals. Furthermore, the functional role usually played by Endozoicomonas in scleractinian corals could be fulfilled by other genera in fire corals (Alteromonas, Halomonas, Pseudomonas). The microbiome communities of such ecologically important, yet understudied, species appear to be distinct from those of scleractinian corals and might help us to get a broader picture of the coral-associated symbiotic diversity involved in reef resilience.