Hydrobiidae is the most diverse and species-rich freshwater gastropod family in the Palearctic. Their diversity in the Caucasus region remains largely unexplored and the phylogenetic relationships with European taxa have not been clarified yet. The primary objective of this study is to perform a molecular phylogenetic analysis of the stygobiotic Hydrobiidae of the Caucasus with an increased taxon sampling and incorporation of multiple molecular markers. We show that the Caucasian hydrobiids are represented by three distinct lineages of a subfamily rank: (1) Caucasopsiinae subfam.nov., comprises most of the stygobiotic hydrobiid genera endemic to Caucasus; (2) Belgrandiellinae includes a single stygobiotic genus Sitnikovia and a complex of crenobiotic genera; (3) Islamiinae is represented by a single monotypic genus. The Caucasian stygobiotic hydrobiids are represented by 13 genera, five of which were identified as new for science, and at least 37 species, including a significant number (20 species) of putative new taxa. Analysis of the soft-body anatomy revealed that the female reproductive system showed the best congruence with the phylogenetic relationships. Shell morphology showed high variability at both inter- and intrageneric level, questioning the generic assignment of species based on empty shells. The Caucasian stygobiotic Hydrobiidae show high endemism at all taxonomical levels from species to subfamilies, which probably reflects their long evolution in relative isolation from the hydrobiid clades inhabiting other regions.