Abstract: ISSR technique was used to investigate the genetic diversity of the 2 Gracilaria algae, including 1 strain G.lemaneiformis from Nanao Island and 17 strains G.tenuistipitata var.liui, which came from west Guangdong waters(3 strains), east Guangdong water (6 strains), Beibu Gulf (3 strains) and Hainai Island (5 strains). Of the 6 ISSR primers screened, 5 primers could produce clear bands. A total of 72 bands were amplified and 57 (79.17%) revealed polymorphism. The data were used to generate Nei′s similarity coefficient (S). The results showed: besides the population of Hainan, there wasn′t any genetic diversity in individuals interpopulation because their genetic similarity were all 1.000, the genetic similarity of population of Hainan was among 0.899~1.000. The genetic similarity were 0.7955~0.8764 among the four geographical populations of G.tenuistipitata.The maximum similarity occurred between Beibu Gulf and East Guangdong waters (S=0.8764). The genetic distance between G.lemaneiformis and G.tenuistipitata was 0.4630.