In this study, analysis of complete structure of mitochondrial D-loop region with its regulatory motifs was investigated in four species of the Acipenser of Caspian sea (A. gueldenstadtii, A. persicus, A. stellatus, A. nudiventris). DNA extraction was done by acetate Ammonium method and PCR reaction were performed by a pair of specific primers for the complete amplification of D-loop along with sequences associated with tRNA-threonine and proline. Sequencing on amplified fragments were was done on both strands. Repetitive sequence of tandem repeat (mini-satellite) was observed in the upstream site of D-loop region after the sequence of tRNA proline in all species except the Ship. The results showed that the central repetitive units of 83-82 pairs with 3.2  repetitions in A. persicus  and A. gueldenstaedtii and 2.4  repetitions in A. stellatus were the reason for the length variation in this region. In addition to the central repeat sequences, there were two more repetitive sequences of 39 and 43 bp in this section, which were also present with 3.2  repetitions. But none of these repetitive sequences was observed in ship. The length of the control region in the A. gueldenstadtii, A. persicus, A. stellatus, A. nudiventris was 921, 870, 826 and 839 bp, respectively. The overall structure of the D-loop region showed that the sturgeon control region is similar to that of other fish, including the homologues of the CSB -conserved  blocks, which are located on the upstream of these blocks. According to the presence of tandem repeat (mini-satellite) in control D-loop region and also the importance of these markers in conservation programs for genetic resources it  may be possible to use them in screening of sturgeon species.