Research on the evolution of the symbiosis between the boring mussel Fungiacava eilatensis (Bivalvia: Mytilidae) and its mushroom coral hosts (Scleractinia: Fungiidae), which requires phylogenetic reconstructions of both the Mytilidae and the Fungiidae, contributes to the understanding of the complexity of coral reef ecosystems. Previously, Fungiacava was regarded as a genus that had descended from Leiosolenus or as belonging to the subfamily Crenellinae, but no phylogenetic support has been obtained for this hypothesis. In the present study, the 18s rRNA sequences of ten mytilid species and the shell microstructures of 12 mytilids were investigated. The phylogenetic position of F. eilatensis is discussed in relation to its associations with its host species. The results of the molecular phylogenetic analysis indicate that F. eilatensis forms a sister group with Leiosolenus simplex, a live-coral-boring species within the Leiosolenus clade. Scanning electron microscope observations indicate that the shell of F. eilatensis is constructed of 3 layers: the outer shell layer with a homogeneous structure, the middle shell layer as a sheet nacreous structure and the inner shell layer with an irregular simple prism structure. This shell microstructure of F. eilatensis is similar to that of Leiosolenus malaccanus and L. simplex. These findings show that F. eilatensis has descended from a coral-boring Leiosolenus species and that it would be adequate for Fungiacava to be treated as Leiosolenus. However, because of its extraordinary shell shape it has been kept as a separate genus.