Abstract: The sequences of the control region (D-loop) of mitochondrial DNA ( mtDNA) were obtained from five species of sturgeon. The sequences obtained had lengths between 795-813 bp. The motifs of the conserved sequence block (CBS) and termination-associated sequence (TAS) were identified in the sequences. Examination of the molecular phylogeny using maximum likelihood, maximum parsimony and Bayesian analysis shows that sturgeons form two clades representing biogeographic distribution, and the Huso is not monophyletic. Heteroplasmy in 150 fishes was due to a variable number of tandem repeats. Length of the central repeat units ranges from 78 to 82 bp with repeat sequence copies between four and six. The repeat units, followed by an imperfect repeat unit, are in high similarity between species, with 82.93% between Amur sturgeon and starlet and 90.59% between Siberian sturgeon and Russian sturgeon. Furthermore, comparing with other repeat sequences published, different species have the same repeat unit and intramolecular recombination event may happen in the repeat unit. All of these indicate that the repeat units are related to the evolution of sturgeon and arose prior to species divergence after which recombination happened.