The Microsatellite DNA technique was applied to assess genetic diversity and genetic differentiation in three wild populations of Apostichopus Japonicus from Yantai,Weihai and Dalian.9 polymorphic loci were screened electrophoretically for genetic variation of the three wild populations.The following parameters were calculated: heterozygosity, polymorphism information content (PIC), effective allele number, allele frequency, genetic distance, genetic identity coefficient, Hardy-Weinberg balance deflection index and so on. Results show that the number of total alleles of these 9 microsatellite loci is 59. The average of allele number in each microsatellite locus of the Yantai 、Weihai and Dalian populations is 6.5556、5.8889 and 6.0000, respectively; the average effective allele number is 4.6033、4.0466 and 4.1367, respectively; The PIC of polymorphic loci varies between 0.5129-0.8794.The average observed heterozygosity (Ho) of three populations is 0.6416、0.6595 and 0.5824 respectively,and the average expected heterzygosity (He) is 0.7641、0.7161and 0.7364, respectively. Cluster analysis of the three wild populations performed with UPGMA(unweighted pair group method with arithmetic mean)confirmed the closer linkage between Weihai and Dalian than their individual distances to Yantai. Key words：Apostichopus japonicus;geographic populations ;genetic diversity;microsatellite DNA