Minnows (genus Phoxinus) are small, cyprinid species of fish, widely distributed throughout Europe and Asia, including in Croatia and neighboring countries. Currently, the genus Phoxinus has as many as 23 different mitochondrial genetic lineages, thirteen described species, while three species have been named, but their status has not yet been confirmed. Until a few years ago, it was thought that two species were widespread in the Western Balkans: Eurasian minnow (Phoxinus phoxinus) and the Adriatic minnow (P. lumaireul). The first investigations showed the absence of the P. phoxinus species in this area and the exceptional diversity of the P. lumaireul species with the existence of new genetic lines and undescribed species. The aim of this doctoral investigation is to provide a more detailed and clearer insight into the phylogenetic and phylogeographic as well as interand intra-species relationships within the genus Phoxinus by a combination of molecular phylogenetics and population genetics methods. The research showed a wide distribution of the species P. lumaireul and a great genetic diversity in the Western Balkans, with the existence of four genetic subclades in the area of Croatia and Slovenia. Two new species of the Phoxinus genus were discovered in Croatia, one of which is new to science. By combining the methods of molecular phylogenetics with morphology and meristics, this species was described as Phoxinus krkae. For the needs of more detailed research on population genetics within the genus, but especially within the P. lumaireul s.l. complex, a new set of microsatellite markers was developed, which will provide detailed insights into mutual population relationships, hybridization events and natural adn human-mediated introgressions.