Deep-sea bivalves of the subfamily Bathymodiolinae (family Mytilidae) are very widespread and form dense beds in reduced environments such as hydrothermal vents and cold seeps. Bathymodiolus mussels recently discovered on African cold seeps strangely resemble Gulf of Mexico and Barbados seep species. This raises intriguing questions regarding their taxonomic relationships and their dispersal capabilities across the Atlantic equatorial belt. The morphological study of the shell and soft parts of mussels from either sites of the Atlantic shows that they form two distinct groups: the Bathymodiolus boomerang group (also including Bathymodiolus heckerae and a species from Africa), and the Bathymodiolus childressi group (also including Bathymodiolus mauritanicus and one species from Barbados). Phylogenetic relationships inferred from the nucleotide sequences of the ribosomal DNA internal transcribed spacer (ITS-2) and mitochondrial cytochrome c oxidase subunit I (COI) confirmed morphological analyses and the existence of two amphi-Atlantic complexes of species. Both ITS2 and COI phylogenies indicate almost no difference between the two eastern Atlantic seep mussels (Bathymodiolus sp. A and B. mauritanicus) and their western Atlantic counterparts (B. boomerang and Bathymodiolus sp. B; Barbados Prism cold seeps). In the B. boomerang complex, B. heckerae seems to differ from the Barbados and the African species, whereas these latter two are not distinguishable. In the B. childressi complex, relationships are less clear and do not support the description of new species from the Barbados. Past and present-day connections across the Atlantic are discussed in the light of both larval dispersal capabilities of the mussels and the equatorial Atlantic circulation to appreciate whether these species could represent true amphi-Atlantic species.