The clitellate branchiate genus Branchiodrilus presently includes three nominal species with a mainly tropical distribution. A recent molecular phylogeny of the subfamily Naidinae suggested that species complexes may occur within the genus. In order to delimit species, we studied a total of 91 Branchiodrilus specimens collected in Asia, Africa and Europe; the genus is introduced in the latter area. We used an integrative approach, where genetic data were analysed for 42 specimens (single‐locus and multiple‐locus methods) and then compared with patterns shown by morphology.Ten Molecular Operational Taxonomic Units could be identified within Branchiodrilus, potentially representing 10 different species. Most of the delimited species are genetically well separated. In contrast, morphological scrutiny identified only three non‐overlapping clusters of specimens, one of them grouping all specimen from the Palaearctic region and belonging to the same species. Other morphological groups are mostly consistent with the biogeographic distribution of species. The Oriental region harbours six species and might be the centre of origin from which Branchiodrilus species have dispersed and radiated. Two other species are present in the Afrotropical region, among them B. cleistochaeta newly obtained from the type locality and genetically characterized, but the presence of B. hortensis in Africa is queried. The taxonomic relevance of the morphological criteria traditionally used to distinguish nominal species is useless at the species level. B. hortensis and B. semperi are now considered as species inquirenda. To document the genital organs of species remains highly desirable, although hardly practicable for this species complex with a primarily asexual reproductive mode.