The genetic diversity of Cristaria plicata were conducted by using mitochondria DNA COⅠ gene as molecular marker. 620 bp lengths of homological fragments in 200 individuals from ten stocks captured in the middle and lower Yangtze River were sequenced. The average contents of A⁺T (60.1%) were significantly higher than those of G⁺C (39.9%). The sequences contained 105 polymorphic nucleotide variable sites, accounting for 17% of the total number of bases. The ratio of transition and transversion was 8.7. Fifty eight haplotypes were defined (GenBank accession number: EU698893-EU698950) in this study, in which Hap-5 was the major haplotype, accounting for 41% of the total individual number. The average nucleotide difference and nucleotide diversity index of Poyanghu population were 25.426 and 0.041 01 respectively, which were the highest. Genetic diversity parameters of Taihu and Quzhou populations were lowest. Based on the genetic distance among populations, Neighbor-Joining (NJ) tree suggested that three populations of Hongzehu were clustered firstly and then clustered with Chaohu population. The second clade comprised Qiantangjiang population, Taihu population, Quanzhou population, as well as Honghu population. The third clade included Dongtinghu population, and finally clustered with Poyanghu population. The fixtion index (F_st) calculated by the analysis of molecular variance (AMOVA) reached to 0.208 1 (P<0.001), indicating that there were some genetic differentiations in different populations of C.plicata in China.