Unisexual forms of lower vertebrates (fish, amphibians, and reptiles) reproduced by parthenogenesis, gynogenesis, or hybridogenesis are represented by diploids, triploids, or tetraploids, whose origin is associated with interspecific hybridization. Among fish species, the highest variability of unisexual polyploids was found in the genus Cobitis. The structure of their genomes and putative parental species holds great interest for the investigation in association with questions about possible evolutionary success. In particular, it serves to elucidate the possible high colonization properties of a few polyploid forms, in contrast to the local history of rather numerous hybrid forms with a limited distribution. Therefore, the aim of this study was to describe the karyotype structure of two newly discovered triploid forms of the genus Cobitis, to analyze their origin and putative parental species. The karyotype structure of 182 spined loach individuals from the Western Dvina River and 91 individuals from the upper Dnieper River of the Smolensk District of Russia was studied. A total of 121 studied individuals from the Western Dvina comprised triploid females with a chromosome number 74 and karyotype consisting of 13 meta-, 39 submeta-, and 22 subtelo-acrocentric chromosomes. Among loaches collected in the upper Dnieper River, 42 triploid females were found with 74 chromosome number including 23 meta-, 26 submeta-, and 25 subtelo-acrocentric chromosomes. Other individuals from both localities were karyologically identified as Cobitis taenia Linnaeus, 1758 with 2n = 48. The triploid form of spined loaches of the Western Dvina River most likely arose as a result of the hybridization of Cobitis tanaitica Bǎcescu et Mayer, 1969 and C. taenia. The range of C. tanaitica, whose karyotype is characterized by an evolutionarily fixed Y-autosomal translocation, is limited to the rivers of the northern coast of the Black Sea. Therefore, hybridization probably happened in late Pleistocene in the Dnieper River system, where both parental species occur. The triploid form that arose here is unique for the Baltic Sea basin. Probably, it colonized the Western Dvina through the artificial Berezinskaya water system (Berezina Canal = Daugava–Dnieper Canal), but at the same time it was forced out of its area of origin by other triploid forms which are now widespread there. According to the karyotype structure, the triploid form, common for both the upper and lower reaches of the Dnieper, has a trihybrid origin, with probable hybridization of Cobitis elongatoides Bǎcescu et Mayer, 1969, C. tanaitica, and yet unidentified species Cobitis sp. Both studied triploid forms are parts of unisexual-bisexual complexes, in which their putative diploid maternal species (C. tanaitica and C. elongatoides) are absent, and the role of the host species involved in reproduction belongs to C. taenia.