Corals form critical associations with microorganisms, which exert numerous beneficial functions for the host and are indispensable for its survival. Due to their ability to evolve rapidly, microbes could also mediate transgenerational acclimatisation of corals in the current face of climate change. In order to gain insight into the biological mechanisms that underlie the functioning of the holobiont and its persistence, it is important to understand how microbes are transmitted and maintained across generations. However, only a handful of studies have investigated the transmission mode of bacteria in corals and processes remain unclear or incompletely understood. Here, we combined amplicon sequencing with fluorescence in situ hybridisation (FISH) in order to investigate the patterns of microbiome acquisition in a precise and reliable approach. This is the first study analysing the microbial community composition at the amplicon sequence variant level and in several coral life stages (parental colonies, newly released larvae and early recruits), in conjunction with FISH to address this question. We were able to capture the identity and abundance of bacteria that were either horizontally taken up from the envrionemnt or vertically inherited from the parents, and microscopy examinations enabled us to confirm the presence of bacterial aggregates inside coral larvae. These results are novel in terms of biological findings and combination of methodologies employed.