Palythoa species have been extensively studied since the 1971 when Moore & Scheuer described the occurrence of palytoxin in P. toxica, explaining the “science” behind the “limu-make-o-Hana” Hawaiian legend. These soft corals are considered holobiont models but the diversity and functional aspects of its microbiota were not thoroughly assessed. In this work we focused on describing the microbiome associated with two species of zoanthids from Palythoa genus, P. caribaeorum and P. variabilis. To achieve that goal we performed Illumina shotgun sequencing of the metagenomic DNA from specimens collected in five locations along the Brazilian coast, considering two different spatial scales, from regional (tens of kilometers) to continental distances (thousands of kilometers).