Kaluga () is the native sturgeon in the Amur river. Similar to other sturgeons, their populations have sharply decreased in recent decades; they have been identified as one of the most endangered species in the world. Unlike the rapid decline of wild populations, sturgeon farming has rapidly increased in China Mainland. The intra-specific hybridization of the female Kaluga and male Amur sturgeon () is widely performed, constituting a large part of sturgeon production in China. In this study, we use the Cyt gene and D-loop region of mitochondrial DNA to assess the genetic diversity of three Kaluga populations, including the wild population from the Amur river, and two populations cultured in national sturgeon breeding farms located in China:one from Fangshan, in Beijing city and the other from Quzhou, in the Zhejiang province. All of the tested individuals were of identical the Cyt haplotype, whereas 9 haplotypes were found in the D-loop region. There was no diversity detected at the nucleotide level on the Cyt d) reached 0.593, but nucleotide diversity () was only 0.00213. There were 6 D-loop haplotypes detected in 8 individuals from the wild population and 5 haplotypes detected in 58 individuals from the cultured populations. The results suggested the wild Kaluga population might have experienced a serious genetic bottleneck. Meanwhile, in the process of artificial propagation of Kaluga, only a few individuals might have been involved in reproduction each time in both the cultured populations. Phylogenetic tree analysis based on partial sequences of the Cyt genes supported the previous results from other researchers. The phylogenetic relationship between and other Pacific sturgeon species was close, but that between was not. Our result implied that the prevalence of the traditional genus was not supported by molecular genetic data.