In present study,genetic differentiation of the Chinese shrimp Fenneropenaeus chinensis between cultured(21 individuals)and wild populations(14 individuals,sequences were downloaded from the GenBank)was investigated using the sequence of mitochondrial control region(CR).Four individuals of theF.merguiensis were chosen as the outgroup during the phylogenetic analysis in this study.Sequences were edited and aligned using DNA Star software and refined manually.Genetic diversity indices such as number of haplotypes,polymorphic sites,transitions,transversions,and indels were obtained using the program ARLEQUIN(Ver. 3.0).Haplotype diversity(h)and nucleotide diversity(л)were calculated with DNASP 4.0.The nucleotide compositions and the average distances between populations and within population were calculated with MEGA 4.0.The Network software was used to draw the minimum spanning tree based on the haplotype data.The results were as follows:the A+T content was higher than the G+C content in both the populations,but the G+C content was a little lower in the cultured population.The results indicated genetic divergence existed between the 2 populations based on the 563 bp sequences.The gene diversity of the wild population(0.967 2)was a little higher than the cultured population(0.938 0).There was no shared haplotype between the 2 populations.The ratio of transitions/transversions of the wild populations and nucleotide diversity were 3.5 and 0.010 6 respectively while they were 4.0 and 0.009 4 for the cultured population.The nucleotide diversity of the wild population was a little higher than cultured population.The K2P distance was 0.010 8 between the 2 populations,0.010 7 in the wild population and 0.009 5 in the cultured population.Both the NJ phylogenetic tree and the haplotype minimum spanning tree showed no significant genealogical structure.The exact test of population differentiation showed that the 2 populations were significantly different(P=0.000 9).The F_ST value between the populations was 0.069 8(P=0.00),which indicated that the difference between 2 populations was significant.This may indicate that some alleles were lost during the aquaculture.