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.