In this paper, we analyzed the mitochondrial and nuclear genomes of Amur sturgeon () and Kaluga () to establish genetic markers that can be used for germplasm identification. In the D-Loop region of the mitochondrial genome, 119 samples from the three known sturgeon species as well as samples from 30 unknown sturgeon species were sequenced. The unknown species were identified by multiple sequence alignment, constructing NJ phylogenetic trees, and calculating genetic distance. In the nuclear genome, fifteen microsatellite markers were used to analyze differences in the genomes of the three known species. Two primers were obtained, Ls19 and SX226, which amplified specific bands in the three known species. In Amur sturgeon, the specific bands of Ls19 amplification products were 126 bp and 130 bp. In Siberian sturgeon, they were 139 bp and 143 bp, and in Kaluga, they were 124 bp and 127 bp. For SX226, the specific band of amplification products was 185 bp in Amur sturgeon. In Siberian sturgeon, the specific bands of SX226 amplification products were 260 bp, 273 bp and 283 bp,and in Kaluga, they were 180 bp and 182 bp. Based on the above results, the unknown sturgeon germplasm samples were identified as:17 , 2 Huso dauricus, and 8 . These results show that the Ls19 and SX226 microsatellite primers can be used in the molecular identification of germplasm from Amur sturgeon, Siberian sturgeon, Kaluga, and their hybrids.