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The phylogeographic analysis of the tubenose gobies from 15 localities included samples from the Sea of Azov basin and the Chornaya River in the Crimea, as well as haplotypes described from variability of mitochondrial cyt b gene fragment and previously deposited in the GenBank database resulted in new taxonomic and zoogeographic hypotheses. The previous hypothesis about marine and freshwater lineages of tubenose goby should be rejected. Really, tubenose gobies from the Black Sea basin are represented by two euryhaline species historically distributed in different areas: Proterorhinus semilunaris in the western part of the Black Sea basin and possibly eastern Aegean basin and P. marmoratus in north-eastern part of the Black Sea basin. P. tataricus is a younger synonym of P. marmoratus. Several rivers and reservoirs in so called Steppe Crimea are populated by P. semilunaris which could spread from the Dnieper River basin through Severo-Krymskyi channel or could be accidentally introduced. The taxonomy of tubenose gobies distributed in the Caspian Sea and Sea of Azov basin, as well as taxonomic status of goby founded in the Chernozemel’skyi channel need further molecular genetic studies of Caspian tubenose goby populations.