Corals are colonized by a wide array of microorganisms including bacteria. While the diversity of coral-associated bacteria has been studied extensively, knowledge about their exact ecological role remains scarce. Bacteria from the genus Endozoicomonas are well-known coral symbionts ubiquitously found as cell-associated microbial aggregates (CAMAs) in a wide range of coral species, however, their spatial distribution and function within the coral holobiont remain largely underexplored. All together 12 distinct genotypes of the reef-building coral Acropora loripes were obtained from two locations in the central Great Barrier Reef. 16S rRNA gene metabarcoding demonstrated that all genotypes harbour Endozoicomonas as their most prevalent bacterial symbiont. Using histology and hybridization chain reaction fluorescence in situ hybridization (HCR-FISH), 311 CAMAs were examined, and taxon-specific probes revealed bacterial clusters to be comprised of members of Endozoicomonas. No significant differences were observed in the occurrence or morphology of CAMAs between reef sites. The eleven most prevalent Endozoicomonas strains were cultured and are currently being genome sequenced, allowing us to investigate their functional potential and develop strain-specific FISH probes to explore whether CAMAs are comprised of one or multiple Endozoicomonas strains. Our work contributes to the understanding of how tissue-associated bacterial communities influence coral holobiont functioning.