Species in the genus Bathymodiolus are mytilid mussels found at deep-sea hydrothermal vents and cold seeps. Next-generation sequencing techniques were employed to identify eighteen unlinked polymorphic microsatellite loci for Bathymodiolus manusensis from Manus Basin in the western Pacific. Allele frequencies for eight loci conform to Hardy–Weinberg expectations and observed heterozygosities ranged from 0.04 to 0.90 (mean H _O = 0.45, SD = 0.25). Ten of eighteen loci cross-amplified in Bathymodiolus heckerae from Atlantic seeps. Microsatellites developed for Bathymodiolus manusensis are being deployed to study connectivity among populations of this species colonizing geographically discrete back-arc basin vent systems.