The marine littoral acarofauna is of interest both in relation to the history of seas and as biological indicators of water quality, but it remains poorly studied. For the first time, we characterize the molecular genetic variability of four widespread, common and abundant species of littoral mesostigmatic mites: Phorytocarpais kempersi, Parasitidae; Halolaelaps celticus and Halolaelaps orientalis, Halolaelapidae; and Thinoseius spinosus, Eviphididae. Based on the nucleotide sequence analysis of nuclear ribosomal repeats (ITS), we studied mite collections from the coasts of the Caspian, Azov, Black, Baltic, White, Barents, Norwegian, Bering, Okhotsk, and Japan seas. The molecular identification of the species studied, based on DNA barcoding using ITS sequences, appears to be clear. We obtained genetic evidence for the separation of Halolaelaps celticus and H. orientalis as two distinct species, based both on clustering their ITS genotypes (separated by 6 parsimony-informative substitutions) and the geographic distributions of their genotypes. The high genetic similarity of the western and eastern Palaearctic populations in both arctic-adapted species, Phorytocarpais kempersi and Thinoseius spinosus, is explicable in terms of their rather recent contact on the northern coast of Eurasia during the last interglacial or Holocene climatic optimum. The high genetic similarity of Halolaelaps orientalis, a relatively thermophilous species, from the Mediterranean region (the Azov, Black, and Caspian seas) with a sample from the very distant Sea of Japan suggests a recent connection between the European and Pacific populations via the Indian Ocean.