This paper presents analytical results of the study of numerous freshwater fish fossils from almost 40 localities in the territory of southeastern Europe. It has been established that freshwater fishes can be regarded as parastratigraphic group suitable for biostratigraphic studies. Ten ichthyofaunal assemblages have been distinguished and characterized in the paper. These assemblages represent successive developmental stages in freshwater fish communities within southeastern Europe during the late Miocene, Pliocene and Pleistocene. Indices of evolutionary transformations (extinction rate, origination rate, taxonomic rotation) for ichthyofaunal assemblages have been calculated, and their trend is discussed herein.