Nine species of the family Cobitidae live in Croatia. Seven species belong to the genus Cobitis and one each to the genera Sabanejewia and Misgurnus. Species such as the C. jadovaensis Mustafić et Mrakovčić, 2008, C. bilineata Canestrini, 1866, C. dalmatina Karaman, 1928, C. illyrica Freyhof et Stelbrink, 2007 and C. narentana Karaman, 1928 live in the Adriatic River Basin (the northern Mediterranean), while the C. elongatoides Bacescu et Maier, 1969, C. elongata Heckel et Kner, 1858, S. balcanica Karaman, 1922 and M. fossilis Linnaeus, 1758 inhabit watercourses of the Danube River Basin. Although most Adriatic taxa appear to be endemic to this area, some researchers have revealed new phylogenetic relationships, suggesting the possibility of more recent taxa exchange with Danube freshwater fish fauna. All members of these genera inhabit either running and/or standing waters. According to IUCN methodology, S. balcanica, C. elongata and M. fossilis in the Danube watershed and C. dalmatina and C. narentana in the Adriatic watershed have been classified as vulnerable. C. elongatoides is in the lower risk category. The newly determined species C. bilineata, C. illyrica and C. jadovaensis will be in the endangered category. Here we present the majority of a total of 20 areas and water bodies included in the proposal of Natura 2000 and which have been selected for the conservation of the species from the family of the Cobitidae.