The investigations carried out in various aquatic ecosystems of the Republic of Moldova, during the years 2004−2019, led to the establishment of the diversity of Gobiidae, which lists 10 species: Benthophilus nudus Berg, 1898; Knipowitschia longecaudata (Kessler, 1877); Mesogobius batrachocephalus (Pallas, 1814); Ponticola eurycephalus (Kessler, 1874); Neogobius fluviatilis (Pallas, 1814); Neogobius gymnotrachelus (Kessler, 1857); Neogobius kessleri (Guenther, 1861); Neogobius melanostomus (Pallas, 1814); Proterorhinus semilunaris (Heckel, 1837) and Gobius niger Linnaeus, 1758. Such species as: Caspiosoma caspium (Kessler, 1877), Knipowitschia cameliae Nalbant et Otel, 1996, Neogobius ratan (Nordmann, 1840), Neogobius syrman (Nordmann, 1840), Benthophiloides brauneri Beling et Iljin, 1927 have not been identified by us, but are mentioned in other scientific sources (Ganea et al., 1981; Cozari et al., 2003; Romanescu, 2012; Moșu et al., 2013). Comparative analysis of the gobiidae ichthyofauna from Dniester River and Prut River revealed a greater diversity and abundance of Gobiidae in the Dnister River than in the Prut river, 10 species versus 6 species. The relative abundances of Gobiidae species in the Lower Dniester sector for the year 2018 captured with juvenile catching trap are: N. fluviatilis (Pallas, 1814) – 4.13%, N. kessleri (Gunther, 1895) – 3.96%, N. melanostomus (Pallas, 1814) – 2.24%, P. semilunaris (Heckel, 1837) – 1.03%, N. gymnotrachelus (Kessler, 1857) – 0.86% and B.nudus Berg, 1898 – 0.17%. In the lower Prut River, in the area of outbreak in the Danube River, for the year 2018, the maximum share in catches was held by N. kessleri (Gunther, 1861) – 4.99% and B. nudus Berg, 1898 – 4.30%, which indicates the active process of expansion of these species upstream on the Prut river. Other species of gobiidae are shown in catches with the following values of dominance: N. gymnotrachelus (Kessler, 1857) – 3.79%, N. fluviatilis (Pallas, 1814) – 3.10% and P. semilunaris (Heckel, 1837) – 1.20%. Acknowledgement: The study was performed within the projects: 15.817.02.27A -AQUASYS, 18.51.07.08A/PS, BSB 027 MONITOX, BSB 165 HYDROECONEX, MIS ETC 1676, MIS ETC 1150.