Molecular phylogenetic analyses revealed no evidence for cospeciation between deep-sea bathymodiolin mussels (Bivalvia: Mytilidae) and their associated thiotrophic (sulfur-oxidizing) bacterial endosymbionts. Host and symbiont tree topologies were not congruent and inferred time-depths of the gene trees were inconsistent, as expected if the mussel hosts are infected by local strains of the symbiont. Evolutionary divergence among the thiotrophs is correlated with geographical distances among sample locations. Apparently these bacteria established a global distribution long before contemporary oceanic barriers achieved their current positions, and before evolutionarily younger mussel hosts diversified into presently recognized species.