Based on morphological examination of rock-, shell-, and coral-boring bivalves in the marine genus Botula, Wilson and Tait (1984) concluded that this genus comprised a single Recent species, Botula fusca (Gmelin, 1791), with a pan-tropical distribution spanning the western Atlantic, Pacific, and Indian Oceans. Variation in shell colour, habitat, depth, and anatomy were determined to reflect variation within this one species. In a subsequent review of Recent and fossil Botula, Kleemann (2007) expressed doubts about a monotypic Botula given “striking morphological differences” between several described species, advocating for the study of soft tissues and application of molecular tools to help resolve species identities. Here, for the first time, we have undertaken a molecular phylogenetic approach to explore species-level relationships within the genus Botula. Our taxon sampling included freshly collected specimens from the Florida Keys National Marine Sanctuary in the context of ongoing research into bioeroding bivalves at reef restoration sites, in addition to previous collections from the western Atlantic, Pacific, and Indian Oceans available at the Florida Museum of Natural History and the Santa Barbara Museum of Natural History. Based on analyses of mitochondrial (COI and 16S rRNA) and nuclear (H3 and 28S rRNA) genes, the genus Botula appears to be monophyletic, with the contentious species currently classified as Leiosolenus kleemanni (Valentich-Scott, 2008) falling within Botula rather than Leiosolenus. High levels of sequence differentiation among samples in this study, including ones previously identified as “Botula silicula”, Botula cinnamomea, “Leiosolenus” kleemanni, and Botula fusca, supported them as distinct species. Our phylogenetic analyses also identified a potential cryptic species within western Atlantic Botula fusca. Increased knowledge of diversity within the genus Botula should lead to a more accurate understanding of the role of these bioeroding species in reef ecosystems.