Amphioxus is the ancestor of vertebrates 5×108 a ago, it is a typical transitional sample of evolution from invertebrates to vertebrates. Inter simple sequence repeats (ISSRs) and random amplified polymorphic DNAs (RAPDs) technologies were applied to detect the genetic variation of 3 bulking samples and individually sampled populations in nowadays Xiamen sea areas (Xiekou, Nanxian and Huangcuo) where the amphioxuses are alive. For the bulking sampled populations, 5 ISSR and 10 RAPD primers generated 357 bands, of which 181 (50.7%) were polymorphic. Nei index and UPGMA statistical analysis indicated that amphioxuses in these 3 areas could be divided into 2 groups. The genetic distance between animals in Nanxian and Huangcuo areas was 0.07 and classified into 1 group, while the population in Xiekou belonged to another group because its genetic distances in Nanxian and Huangcuo were 0.12 and 0.14, respectively. The result was in accordance with the morphological comparison among animals from those areas. For individually sampled population, Shannon’s index of genetic diversity was used to partition the diversity of the animals among these 3 sea areas, and the results showed that the indices in populations of Xiekou, Nanxian and Huangcuo, were 0.583, 0.482 and 0.374, respectively. The linear regression equation analysis for amphioxus’ genetic diversity versus the environment factors revealed that granularity/sorting coefficient and water depth were the most important factors that affect amphioxus genetic diversity. On the basis of the results, the suggestions for amphioxus resource conservation in Xiamen sea areas are put forward.
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