Water mites of the Hygrobates fluviatilis-complex are often the most ubiquitous and usually the most abundant water mite group in the running waters of the Palaearctic and Balkans. In the present study we used an integrative taxonomic approach by applying partial COI sequences (DNA-barcodes) to describe two new species of the fluviatilis-complex from the Balkan Peninsula, H. balcanicus Pešić sp. nov. (Bulgaria, North Macedonia, Greece) and H. mediterraneus Pešić sp. nov. (Montenegro). Phylogenetic analysis based on COI data placed H. balcanicus sp. nov. as the sister species of the clade grouping H. turcicus Pešić, Esen & Dabert, 2017 and H. ulii Pešić et al. 2019 whereas H. mediterraneus sp. nov. is placed as the sister species of H. grabowskii Pešić et al. 2019, with about 20% and 13% K2P divergence, respectively, between the closest relatives.