Protists are less studied for their role and diversity in ecosystems. Notably, protists have played a key role as endosymbionts in corals. Using metabarcoding with anti-metazoan primers, we characterized the eukaryome (microeukaryotic fraction of the microbiome) of two coral species across the Caribbean and Pacific and showed that host species and geographic region determine the eukaryome composition. In addition to Symbiodiniaceae and corallicolids, we identified numerous other protist lineages associated with corals, including many that are poorly characterized.