Corals house a variety of microorganisms which they depend on for their survival. Microbes associated with corals include dinoflagellates of the family Symbiodiniaceae, which provide their hosts with most of their carbon requirements, as well as numerous bacteria. While coral-microorganism interactions are widely studied, interactions between the microbes themselves are only just beginning to receive attention. The study of microbe-microbe interactions in corals is however essential to fully understand the microbiome’s implication in coral health, as well as its ability to cope with climate change. Here, we focused our efforts on interactions between Symbiodiniaceae and bacteria. First, we showed through scanning electron microscopy and fluorescence in situ hybridisation (FISH) the presence of intracellular and cell surface-associated bacteria in a wide diversity of Symbiodiniaceae species, both in laboratory cultures and in Symbiodiniaceae freshly isolated from the anemone Exaiptasia diaphana and the coral Galaxea faciscularis. Further, by combining 16S rRNA gene metabarcoding data, FISH results, and culturing methods, we characterized the bacterial diversity across the Symbiodiniaceae species, and particularly intracellular communities. Intracellular bacteria were highly similar across a wide range of Symbiodiniaceae species, suggesting they may be involved in Symbiodiniaceae physiology, and in turn coral health. Because of their proximity with Symbiodiniaceae, and thus excessive reactive oxygen species produced during a thermal stress event, intracellular bacteria could represent ideal candidates for coral bleaching mitigation through microbiome manipulation.