We analyse the taxonomic structure of the Hygrobates nigromaculatus-complex from the Balkan Peninsula. We describe two new species: Hygrobates lacrima Pešić sp. nov. (Montenegro) and H. limnocrenicus Pešić sp. nov. (Montenegro, North Macedonia). Although both species are morphologically similar, the average K2P-distance between DNA-barcode sequences from H. limnocrenicus sp. nov. and its closest relative H. setosus was 12.43% (SD = 1.47), and between H. lacrima sp. nov. and its closest relative H. nigromaculatus 15.87% (SD = 1.74). The new species exhibit distinct differences in terms of habitat preference: H. lacrima sp. nov. inhabits pools and shallow eddies along faster flowing waters, whereas H. limnocrenicus sp. nov. prefers deeper, fast flowing water, typically found in the outflow of a limnocrenic springs or lake outlets. The finding of these two new species suggests that efforts to investigate mites of the H. nigromaculatus-complex in the Balkans should be intensified.