Danube salmon is an indigenous species, endemic to the Danube basin and it is on the IUCN Red List as an endangered species. The biggest reason for its endangerment is habitat fragmentation caused by the construction of dams and barriers on watercourses, which has caused the reduction and disappearance of populations. Although population size has decreased by two thirds since the end of the 19th century, stable populations of Danube salmon in Croatia have been recorded on the border with Slovenia in Kupa and on the border with Bosnia and Herzegovina in Una. The aim of this study was to describe the genetic structure of Danube salmon in Croatia, to determine the degree of intraspecific and intrapopulation genetic diversity, to assess the origin of individual populations of Danube salmon and their diversity in relation to other European populations and to investigate the evolutionary history of Danube salmon in Croatia. Phylogenetic reconstruction based on sequences for the cytochrome b (cyt b) and rhodopsin (rhod) gene was performed using the maximum parsimony (MP) method and maximum probability (ML) method. The resulting phylogenetic trees and network determined the existence of an evolutionarily separate lineage for Danube salmon. A clear separation of the genus Hucho within Salmonidae was determined. It was found that the genetic diversity of Danube salmon in the Danube basin is very low and that migrations between populations are minimal or non-existent. Low genetic diversity is the result of overfishing and the construction of dams in watercourses, which causes habitat fragmentation.