With the family Polyodontidae, Acipenseridae are the only living members of the order Acipenseriformes. They are amongst the most primitive bony fish and are also the last surviving members of the almost extinct superorder of Actinopterygii - Chondrostei. Different anthropogenic pressures, in combination with their relatively high ecological vulnerability, have led Acipenseridae to a quite unfavorable position, so most countries have started implementing measures for their protection. Historically, there have been 8 recorded species from the family Acipenseridae and 1 from the family Polyodontidae in Croatia, of which only 2 still exist in the wild, both being classified in endangered IUCN categories. The biology of Acipenseridae in Croatia isn't researched enough, which poses a problem in conservation efforts. Gaining insights into their taxonomic and genetic diversity and geographic distribution is the first step for conducting research which will lead to adequate protection of these endangered species. This research uses methods of molecular analysis of the gene marker cytochrome b on species of sterlet and sturgeon captured in the wild and from a fishery. Reconstructions of phylogenetic trees using maximum parsimony and maximum likelihood methods, as well as a reconstruction of their phylogenetic network using mutual joining method and a reconstruction of their evolutionary history using Bayesian methods were made. Measures of their genetic diversity were also calculated. The results confirm that the sampled individuals belong to Acipenser ruthenus and A. baerii species and indicate a much higher degree of genetic diversity of wild populations in comparison to populations bred in fisheries.