Abstract: Total DNA were extracted from the pearl oyster Pinctada fucata tissues preserved at －70℃ and fixed in 95% alcohol, respectively. The results showed that the quality of DNA extracted from alcohol preserved tissue through washing with distilled water was as good as that from frozen tissue. The condition for RAPD analysis was optimized and the appropriate reaction was as follows: a 20 L reaction includes 20 ng template DNA, 1PCR buffer, 0.1 mmolL-1 dNTPs, 2.5 mmolL-1 MgCl2, 0.2 molL-1 each primer, and 1 U Taq DNA polymerase. The optimal annealing temperature is 40℃. The PCR products were separated using non-denatured polyacrylamide gel electrophoresis (PAGE) with silver staining and agarose electrophoresis with ethidium bromide staining, respectively. Both PAGE and agarose separation presented consistent common bands but PAGE can reveal more polymorphic bands.