ISSN 0032-9452, Journal of Ichthyology, 2013, Vol. 53, No. 9, pp. 702–712. © Pleiades Publishing, Ltd., 2013. Original Russian Text © D.A. Medvedev, P.A. Sorokin, V.P. Vasil’ev, N.V. Chernova, E.D. Vasil’eva, 2013, published in Voprosy Ikhtiologii, 2013, Vol. 53, No. 6, pp. 687–698. 702 Although extensive research has been carried out, phylogenetic relations between representatives of the family Gobiidae from the Ponto-Caspian basin, as well as their taxonomic relationships at the supraspe- cific level, are still widely discussed. All species of endemic Ponto-Caspian (Sarmatian) gobies have been described in the genus Gobius (as the majority of other species within this family), which was subdi- vided, regarding the Ponto-Caspian, into seven sub- genera by Iljin (1927) based on morphological fea- tures: Mesogobius Bleeker, 1874; Babka Iljin, 1927; Macrogobius De Buen, 1930; Apollonia Iljin, 1927; Gobius Linnaeus, 1758; Ponticola Iljin, 1927; and Neogobius Iljin, 1927. The Grass goby Gobius ophio- cephalus Pallas, 1814, was placed in a separate genus Zostericola Iljin, 1927, and because this name had been preoccupied, it was then replaced by Zosterisessor Whitley, 1935. Berg (1949) separated relict Sarmatian gobies from the genus Gobius into a single genus Neogobius Iljin. Iljin (1956) and Svetovidov (1964) reported that such division was controversial; the latter assigned the majority of species endemic for the Ponto-Caspian basin to the genus Gobius, thus, recog- nizing the following genera as separate: Proterorhinus Smitt, 1899; Benthophilus Eichwald, 1831; Bentho- philoides Beling et Iljin, 1927; and Caspiosoma Iljin, 1927. The groundlessness of separating the genus Neogobius was later proved based on the analysis of morphological and karyological data (Vasil’eva, 1996, 1999). Nevertheless, the genus Neogobius as compris- ing species from the subgenera Babka, Apollonia, Pon- ticola, Neogobius s. stricto, Eichwaldiella Whitley, 1930, and Chasar Vasil’eva, 1996, was later accepted by the majority of investigators (Miller, 1986, 2003; Vasil’eva, 2003; Bogutskaya and Naseka, 2004). From this moment on, when the results obtained during the analysis of a number of mitochondrial genes demon- strated that the genus Neogobius sensu Berg, 1949, was a paraphyletic group (Stepien et al., 2005; Stepien and Tumeo, 2006), many subgenera within it were raised to generic rank (Stepien and Tumeo, 2006; Neilson and Stepien, 2009a; Diripasko et al., 2011; Patzner et al., 2011). Regarding the Grass goby, some investigators still assign it to the genus Gobius (Vasil’eva, 2003, 2007), while others place it into the genus Zosterisessor (Bogutskaya and Naseka, 2004; Miller, 2004; Kottelat and Freyhof, 2007; Diripasko et al., 2011). The latter variant was also approved by Neilson and Stepien (Neilson and Stepien, 2009a), even though the grass goby on their phylogenetic trees is posited into the same clade as species from the genus Gobius. Taxo- nomic relationships of some other gobies from the Ponto-Caspian are also questioned by different researchers. The aim of this work is to specify phylogenetic rela- tions of Ponto-Caspian gobies based on the analysis of variations in cytochrome b gene within the popula- tions from different parts of their areas under study and to estimate new data from the point of different taxonomic hypotheses. Reconstruction of Phylogenetic Relations of Ponto-Caspian Gobies (Gobiidae, Perciformes) Based on Mitochondrial Genome Variation and Some Problems of Their Taxonomy D. A. Medvedev a , P. A. Sorokin a , V. P. Vasil’ev a , N. V. Chernova b , and E. D. Vasil’eva c a Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia b Zoological Institute, Russian Academy of Sciences, St. Petersburg, Russia c Zoological Museum, Moscow State University, Russia e-mail: vas_katerina@mail.ru Received June 7, 2012 Abstract—Phylogenetic relations of Ponto-Caspian gobies in the context of different taxonomic hypotheses have been studied based on the analysis of variations in cytochrome b gene. Evidence for the paraphyly of the genus Neogobius sensu lato, represented by two independent phyletic lineages that should be treated as sepa- rate genera Neogobius s. stricto (includes a species group of N. melanostomus–N. fluviatilis–N. caspius) and Ponticola, has been provided. It has been demonstrated that the Racer goby N. gymnotrachelus refers to the latter genus. It is proved that the Grass goby Gobius ophiocephalus belongs to the genus Gobius s. stricto. DOI: 10.1134/S0032945213060064 Keywords: gobies, Gobiidae, phylogenetic relations, cytochrome b, taxonomy