A total of 21 invasive species are recorded in ichthyofauna of the Cheboksary reservoir and water bodies of its basin. Nine-spined stickleback Pungitius pungitius (L., 1758) is one of naturalized species which is spreading in the territory of the Middle and Upper Volga. In our opinion, nine-spined stickleback is an undesirable invader. That is why the morphological characteristics and intraspecific phenotypic variability of the species P. pungitius in the basin of the Cheboksary Reservoir are of interest from the point of view of population ecology. P. pungitius naturalized successfully in the Ushakovka River, Nizhny Novgorod oblast. In 2011–2012, nine-spined stickleback was recorded in the Sundyr and Malaya Yunga rivers in the Republic of Mari El. When studying the morphometry of stickleback, measurements of 33 characters were made in mature and immature speciments. The feeding patterns of stickleback were also studied. A comparative analysis was conducted of the complex of morphological characters (30) of P. punginius from the local populations in the basin of the Cheboksary reservoir and the “native” population (Lakes Sarannoye and Gavanskoye of Bering Island (Commander Islands)).