Abstract: Levels of genetic variation in the sea cucumber, Stichopus japonius , were determined by vertical polyacrylamide gel electrophoresis and compared with 6 population (including 5 natural stocks and 1 cultured stock) from coastal water of the northern China. Polyacrylamide gel electrophoresis was used to detect expression of isozymes in the intestines, body walls, respiratory trees. MDH (Malate dehydrogenase), EST(Esterase), SOD(Superoxide dismutase), CAT (Catalase), ME(Madic enzyme), ACP(Acid phosphatase), ALP(Alkaline phosphatase), ADH(Alcohol dehydrogenase), LDH(Lactate dehydrogenase) were determined, and the enzymatic activity in SOD, CAT, MDH and EST was shown to be coded by 8 gene loci, namely, Sod, Cat, Mdh-1, Mdh-2, Est-1, Est-2, Est-3, and Est-4, seven loci being polymorphic with the mean proportions of 87.5%. It was shown that high genetic variation has been maintained in Stichopus japonicus , and CAT,MDH,SOD and EST could be effective genetic markers to analyze the biochemical genetic structure of Stichopus japonicus . The basic map and biochemical genetic analysis provide basic data for understanding the genetics of Stichopus japonicus population.