Abstract:The base composition and sequence variation of 16S rRNA in the populations of S.fukienense and S.xiusuiense were studied by the methods of PCR and DNA sequencing.We obtianed 513 bp nucleotide sequence by comparison and analyzed the genetic differentiation between S.xiusuiense and S.xiusuiense.The averag genetic distance(P) between the two population was 0.032 ± 0.006, the index of genetic differentiation (Fst) was 0.70336 and the gene flow (Nm) was 0.11.The molecular biology result showed a high degree of differentiation between S.xiusuiense and S.fukienense. There is no gene flow between them.Phylogenetic reconstruction shows the formation of two independent branches of the respective populations, it is consistent with their difference of their shape .