An experiment was conducted to screen molecular markers that can be used for classification of populations of cultured freshwater crayfish samples collected in Anhui, China. After genome extracting, PCR amplifying and sequencing of COⅠ, 16S rDNA, D-loop, Cyt b and 12S rDNA of the samples were performed, and the neighbor-joining phylogenetic tree and genetic distance in MEGA6.06 were used to compare the samples with 30 species recorded in GenBank. The reliability of neighbor-joining phylogenetic tree was tested by 1 000 times bootstrap and the genetic distance was calculated based on kimura-2-parameter nucleotide substitution model. In the neighbor-joining phylogenetic tree (Fig. 1) constructed with Procambarus clarkii as an outgroup, the samples first clustered together with red claw crayfish (Cherax quadricarinatus) and then constituted a relationship to other species, strongly showing that the samples should be classified as C. quadricarinatus. The genetic distance range (Table 3) showed that the average genetic distances of 16S rDNA, Cyt b and 12S rDNA were increasing from intraspecific individual to intra order interfamily, and were not at the same level, so that they can probably be better used in cultured population. The results from this paper will benefit the people working in the crayfish farm, and provide reference for classification of freshwater crayfish in the future.