Dead coral rocks are prevalent hard substrates in shallow warm waters, providing habitat for various infaunal and boring invertebrates. Despite this, the nature of species interactions, especially symbiotic relationships, among them remains poorly understood. Bonellia (Annelida: Thalassematidae: Bonelliinae) is a group of greenish echiuran worms commonly inhabiting cavities inside dead coral rocks. Although echiuran burrows in marine sediments are known to harbour various host-specific macrosymbionts, it remains unclear whether such associations also occur in hard substrates. To address this, we investigated the diversity of macrosymbionts associated with the burrows of Bonellia sp. aff. minor in the warm-temperate coast of the Kii Peninsula, Japan, and the evolutionary origins of those symbionts. The host’s burrow morphology was also examined using micro-computed tomography (CT) scanning. Our field survey revealed that the burrows of Bo. sp. aff. minor hosted three commensal species including a polychaete, Oxydromus fauveli, and two new species, a bivalve (Basterotia bonelliphila sp. nov.) and an amphipod (Leucothoe bonelliae sp. nov.). Our molecular phylogenetic analyses showed that each symbiont species belongs to a clade comprising commensal species specific to echiurans or annelids. Overall, our findings contribute to a better understanding of symbiotic associations in marine hard substrates.