Abstract: The random amplified polymorphic DNA (RAPD) technique was applied to analyze intra-species differentiation among Tegillarca granosa populations distributed to the south and north of Fujian province.Samples were collected from the south (Shantou and Zhanjiang in Guangdong province) and the north (Wenling in Zhejiang province,and Korea),and defined as the representatives of the southern populations (SP),and northern populations (NP),respectively.Amplified with 20 random primers,we acquired 103 distinguished RAPD loci,ranging from 250 bp to 2500 bp in size.The least genetic distance between SP and NP was 0.3261-0.4511,while that within the populations of NP or SP was only 0.0612-0.0692.The inbreeding coefficient (Fst) between SP and NP was also larger than that within SP and NP.Using NJ and UPGMA methods,we also found the nearest phylogenetic relationship consistently occurred within the populations of the SP or NP.A significant intra-species genetic differentiation has occurred between SP and NP,probably due to the geographical isolation between the populations.