Euendolithic, or true‐boring, cyanobacteria actively erode carbonate‐containing substrata in a wide range of environments and pose significant risks to calcareous marine fauna. Their boring activities cause structural damage and increase susceptibility to disease and are projected to only intensify with global climate change. Most research has, however, focused on tropical coral systems, and limited information exists on the global distribution, diversity, and substratum specificity of euendoliths. This metastudy aimed to collate existing 16S rRNA gene surveys along with novel data from the south coast of South Africa to investigate the global distribution and genetic diversity of endoliths to identify a “core endolithic cyanobacterial microbiome” and assess global diversification of euendolithic cyanobacteria. The cyanobacterial families Phormidesmiaceae, Nodosilineaceae, Nostocaceae, and Xenococcaceae were the most prevalent, found in >92% of categories surveyed. All four known euendolith clusters were detected in both intertidal and subtidal habitats, in the North Atlantic, Mediterranean, and South Pacific oceans, across temperate latitudes, and within rock, travertine tiles, coral, shell, and coralline algae substrata. Analysis of the genetic variation within clusters revealed many organisms to be unique to substratum type and location, suggesting high diversity and niche specificity. Euendoliths are known to have important effects on their hosts. This is particularly important when hosts are globally significant ecological engineers or habitat‐forming species. The findings of this study indicate high ubiquity and diversity of euendolithic cyanobacteria, suggesting high adaptability, which may lead to increased community and ecosystem‐level effects with changing climatic conditions favoring the biochemical mechanisms of cyanobacterial bioerosion.