Endolithic bacteria and microalgae live inside coral skeletons playing important functional roles in reefs’ calcium carbonate budget and nutrients cycling. Some keystone endolithic taxa have been reported to have cosmopolitan distributions as many other marine microbes, but highly different endolithic communities have also been observed at small spatial scales. Quantifying the turnover of endolithic species across space and understanding the factors driving their distributions can give insights into the processes underlying the functional and species diversity of the coral microbiome. Here we investigate the distribution of prokaryotic and eukaryotic endolithic communities within individual coral colonies and across short geographical distances by testing how community similarity changes with distance at small spatial scales (0.4cm – 4m). We then investigate how community composition changes from small to global spatial scales (0.4cm – 17,000km) and test the relative importance of niche specialization versus stochastic processes on their distribution. The results indicate that stochastic processes and dispersal limitation create an unexpectedly high rate of bacterial species turnover within colonies. These findings imply that high-resolution biodiversity assessments are essential to understand the composition of the coral microbiome and its ecological roles. Geographical distance did not impact the community composition at larger spatial scales though. Niche specialization seems to underlie the global distribution of endolithic microbes.