Three species of the Eurasian family Cobitidae are distributed in Slovakia. In the present paper, we describe the coenological affinity of Cobitis elongatoides, Sabanejewia balcanica and Misgurnus fossilis in two distinct zoogeographical regions, Slovak Tisza and Danube basins and discuss possible differences of their biotop affinity and habitat preferences. The occurrence of S. balcanica is restricted to primary biotopes with harder substratum particles. Typical species assemblages for the rheophilic C. elongatoides are eurytopic and limnophilous species. C. elongatoides is mostly distributed in primary biotopes, such as rivers and channels. It also occurs in secondary biotopes (drainage canal or pit). M. fossilis is distributed mostly in the secondary biotopes, but it is also found in the primary biotopes. Both species prefer fine substratum, but spatial distribution of the two species is different. C. elongatoides prefers harder substratum of sandy particles mixed with mud or detritus and living vegetation, whereas M. fossilis prefers muddy substratum mixed with detritus and dead vegetation.
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.