To compare genetic markers for population genetics analysis, allozyme electrophoresis and random amplified polymorphic DNA (RAPD) were used to detect the genetic structure of scallop Chla- mys farreri population. Thirteen enzymes (MDH, ME, IDH, GPI, PGM, PEP-LG, PEP-PP, ACP, AK, PK, AAT, SOD, EST) in three buffer systems (TC, pH6.9; TMME, pH 7.4; and EBT, pH8.9) were selected and 22 loci were used for the analysis, among them 7 loci (Gpi, Pgm, Pep-LG-1, Pep-PP, Aat-2, Est-2, Est-3) were polymorphic which attributed 31.82% to the total. The average of heterozygosity was 0.113 and most of the studied loci showed heterozygote deficiencies. The same specimens were investigated using 10 arbitrarily selected primers (10-base). Twenty two of 54 RAPD fragments were polymorphic with av- erage heterozygosity of 0.194. The result indicated that the two types of markers reflected a consistent trend in the parameter values of genetic diversity of the population, but RAPD revealed more information of genetic variation than allozyme electrophoresis. To compare genetic markers for population genetics analysis, allozyme electrophoresis and random amplified polymorphic DNA (RAPD) were used to detect the genetic structure of scallop Chlamys farreri population. Thirteen enzymes (MDH, ME, IDH, GPI, PGM, PEP-LG , PEP-PP, ACP, AK, PK, AAT, SOD, EST) in three buffer systems (TC, pH 6.9; TMME, pH 7.4; and EBT, pH 8.9) were selected and 22 loci were used for the analysis , among them 7 loci (Gpi, Pgm, Pep-LG-1, Pep-PP, Aat-2, Est- 2, Est- 3) were polymorphic which attributed 31.82% to the total. The average of heterozygosity was 0.113 and most The same specimens were investigated using 10 arbitrarily selected primers (10-base). Twenty two of 54 RAPD fragments were polymorphic with av- erage heterozygosity of 0.194. The result indicated that the two types of markers a consistent trend in the parameter values ​​of genetic diversity of the population, but RAPD revealed more information o f genetic variation than allozyme electrophoresis.