The corallivorous Coralliophila meyendorffii (Muricidae, Coralliophilinae) inhabits shallow waters of the northeastern Atlantic and the Mediterranean Sea. Its coral host Parazoanthus axinellae (Zoanthidea, Parazoanthidae), a common Anthozoa of the Mediterranean Sea and the NE coasts of the Atlantic, is an interesting colonial hexacoral lacking a calcareous skeleton. In this study, for the first time, by utilizing the metabarcoding 16S rRNA gene, we investigated on the microbial community associated with the ectodermal mucus and tissue of P. axinellae and the gut of C. meyendorffii. Although 16S metabarcoding based on hypervariable regions proved to be useful as a means of assessing the diversity of microbial communities, its application at lower taxonomic levels is still somewhat limited largely owing to the low evolutionary rates of the 16S rRNA gene. Collectively, our work strengthens the need for continuing efforts to evaluate the microbial communities of peculiar corallivorous neogastropods and their coral hosts.