Several coral genera are known to contain tight clusters of bacteria within their tissues, called cell-associated microbial aggregates (CAMAs), yet little is known about their composition and role. We analysed the location, structure, composition and functional potential of CAMAs in the coral Pocillopora acuta. Using fluorescent in situ hybridisation, we showed that CAMAs are widespread in the tentacles of several P. acuta genotypes. We also uncovered that larvae of some genotypes, but not all, possess CAMAs, suggesting that they can be vertically transmitted. Transmission electron microscopy was applied to further analyse the structure of these aggregates and showed the presence of a membrane surrounding the CAMAs. To assess their taxonomic affiliation and functional potential, CAMAs were isolated using laser-capture microdissection in both larvae and adults and analysed using 16S rRNA gene metabarcoding and metagenomics. Metabarcoding detected two genera in the Endozoicomonadaceae family, Kistimonas and Endozoicomonas. Metagenomic results are pending but will be presented. In sum, the location of these bacteria inside the coral tissues and possibly within a host membrane along with their potential vertical transmission, makes them of great interest for microbially mediated conservation strategies. Understanding their function within the coral holobiont will provide further insight into their suitability.