This research addresses the pressing issue of protecting endangered lamprey species in Croatia, a crucial element in preserving biodiversity, particularly in the face of increasing human-induced impacts on natural ecosystems due to global warming. Lampreys, a group of vertebrates with an ancient lineage, are not fully understood taxonomically, posing a challenge to conservation efforts. In the Danube and Adriatic basins of Croatia, where lampreys are found, the lack of modern molecular methods and analyses has hindered an accurate determination of species numbers. This study aimed to bridge this knowledge gap by assessing the genetic diversity and structure of identified lamprey species and lineages in Croatia using the gene for cytochrome b. The research revealed four distinct lineages within the species Eudontomyzon vladykovi Oliva and Zanandrea, 1959 and confirmed the presence of the species Eudontomyzon danfordi Regan, 1911 in Croatia. Genetic diversity and differentiation tests, coupled with molecular diagnostic analyses, indicated moderate to high levels of genetic diversity within and between the identified species and lineages, emphasizing the deep structuring within Eudontomyzon vladykovi species. These results highlight the significance of understanding lamprey taxonomy and genetic diversity for effective conservation. The study provides important insights into the intricate relationships and conservation needs of lampreys, and provides a basis for future discussions involving additional genetic markers. By gaining a comprehensive understanding of the taxonomy, ecology, and genetic diversity of lampreys, we can ensure their conservation and that of associated ecosystems.