Background: Lake Baikal is the deepest and most voluminous lake in the world, with a unique environment (ultraoligotrophic and well-oxygenated waters at all depths), and is located in a region that is experiencing rapid climate change. It is populated with an endemic genus of oligochaetes (Baikalodrilus), which currently comprises 21 morphospecies. However, the validity of many species is questionable; the great similarity in their description and the lack of unequivocal diagnostic characters often lead to inconclusive species identification. In order to clarify the systematics of this genus, we analysed one nuclear (ITS) and two mitochondrial (COI and 16S) markers of 33 Baikalodrilus specimens and four specimens of the genera Spirosperma, Embolocephalus, Rhyacodrilus and Haber as an outgroup. Results: Phylogenetic inferences based on parsimony, maximum likelihood and Bayesian analyses showed an early separation between two groups of species that belong to two distinct size classes and helped to re-evaluate the validity of some morphological characters as specific diagnostic characters. Three species identified prior to molecular analyses were consistent with clustering based on DNA sequences. A fourth morphospecies proved to be actually an assemblage of two distinct species. It was also possible to isolate a group of specimens that could be considered as a new species. Other clusters remained ambiguous, not only in terms of molecular clustering but also of morphological distinctness. Significance: These results will be useful for a taxonomical revision of the genus and a better assessment of the oligochaete species diversity in a lake environment facing contemporary climatic changes.