Genetic diversity of three pure populations of Cobitis elongatoides from hydrologically and geographically different drainage areas, the Lužnice River (48.49.60 N, 14.55.60 E, Labe River drainage area, North Sea basin), the Nová Říše reservoir (49.09.11 N, 15.32.464 E, Morava River drainage area, Black Sea basin), and the Ida River (48.32.284 N, 21.03.421 E, Tisza River drainage area, Black Sea basin) was evaluated by sequencing of mitochondrial cytochrome b gene. Species identification of unknown Cobitis samples from Vipava River drainage area in Slovenia was also performed based on cytochrome b sequence. All forms of the genus Cobitis are protected by national legislatives and, in accordance with the Council Directive No. 925/43/EEC, they enjoy protection in selected localities of European importance. In total, 11 haplotypes of Cobitis elongatoides were found in Czech and Slovak waters, manifesting low overall genetic diversity. Samples from Vipava River drainage area were identified as Cobitis bilineata.
In Slovakia, Cobitis elongatoides (Bacescu et Mayer, 1969), Sabanejewia balcanica (Karaman, 1922), and Misgurnus fossilis (Linnaeus, 1758) are protected by national legislative, and localities of European importance have been delimited for these species within the Natura 2000 system. In Slovakia, the three species only occur in the Black Sea river system (the Danube and Tisza R. basin). Of them, C. elongatoides is the most widely distributed and most numerous both in its pure form and its hybrid, diploid-polyploid complexes (C. elongatoides x C. tanaitica). It occurs in proper streams and in natural as well as in artificial aquatic habitats, above all, in lowland regions. Comparing data on this species from 1955–1965, no major changes have been found. S. balcanica occurs chiefly in the middle reaches of rivers, first of all, in the Bodrog drainage area (the Laborec, Ondava, Topľa R.) in eastern Slovakia. In the western part of Slovakia (the Danube river system) the occurrence of this species is distinctly less frequent and insular. The distribution of the species has been markedly affected by water pollution, construction of dams and reservoirs, and river bed modifications. The occurrence of M. fossilis is almost exclusively limited to the lowland regions of eastern Slovakia and the Danube Lowland. In those regions, the amelioration measures taken during the second part of the 20th century caused the original natural wetlands to vanish – together with the occurrence of this species. However, M. fossilis found a secondary suitable environment in man-made hydro-amelioration channels, earth pits, and fishponds.