Mitochondrial D-loop sequences were analyzed to study the genetic structure of the sea cucumber Apostichopus japonicus.In this study, 71 individuals from three natural populations were collected from Dalian, China(CD), Rajin, North Korea(KN) and Vladivostok, Russia(RV).447-465 bp D-loop sequences were obtained using PCR amplification.The mean content of A+T(59.2%) was higher than G+C.The proportion of polymorphic sites was 24.24%, in which parsimony informative sites were 53.Forty haplotypes were identified from 71 samples, among which 7 haplotypes were shared by three populations.Genetic diversity parameters showed high genetic diversity among populations.The fixation indices(F_ST) of analysis of molecular variance(AMOVA) within populations was 93.04%, which indicated that the genetic differentiation of the three populations was weak or only moderately differentiated.The genetic distances among populations were 0.037 4(KN and RV) and 0.042(CD and RV).The molecular phylogenetic tree was constructed with the D-loop sequences of Qingdao(QD) and Weihai(WH) from GenBank with NJ method using software MEGA 4.0.Populations of QD and WH clustered into a small branch, then with CD, while KN and RV clustered into the other branch.The results were consistent with their geographical isolation mode.