Abstract:The study on genetic similarity characteristics and distribution has positive significance for biodiversity protection and maintain of forest ecological service function. A 400 m2 fixedplot of Rhizophora stylosa was selected in Gaoqiao, Zhanjiang,Guangdong, and two molecular marker techniques of ISSR (Inter simple sequence repeat) and SRAP(Sequence-related amplified polymorphism) were used to study. Ten ISSR primers and 14 SRAP primers were selected and used for PCR amplification, and 73 and 111 discernible fragments were amplified, respectively.The polymorphic loci were 60 and 88, and the percentage of polymorphic loci were 82.2% and 79.3%. Genetic similarity coefficient ranged from 0.321 to 0.741, and genetic similarity average was 0.563, D-value was 0.414 in fxed plot of pure R. stylosa.At the level of 0.55 similarity coefficient, they were divided into three groups. The genetic similarity was Group 1 > Group 2 > Group 3, and the variation of genetic similarity was Group 1 > Group 2 >Group 3. At the level of 0.6 similarity coefcient, they were mainly divided into eight groups. At the level of 0.55 similarity coefcient,the degree of aggregation of R. stylosa was stronger, the genetic similarity was higher, and the variation degree of genetic similarity was lower. R. stylosa community quadrat in Gaoqiao belonged to different groups with genetic differences, and had a certain amount of gene exchange. The genetic relationship was between distant and near distribution section, and the genetic similarity and variation were moderate. The Group 3 was calculated to be the most dominant. It was preliminarily proved that the aggregation of R. stylosa was directly proportional to the genetic similarity, and inversely proportional to the genetic similarity variation.