80 pairs of SRAP primer were used to analyze the genetic relationship among 16 Jincheng（Citrus sinensis Osbeck） germplasms from Chongqing area.The results showed that the genetic relationship between different Jincheng species was very close.In the PCR amplification,only 30 pairs of primers (37.5%) were polymorphic.56 polymorphic bands were obtained,with an average of 1.87 band each pair of primers.Results of cluster analysis showed that the genetic relationship between Baleng Cheng and Changye Cheng was more far than that between other types.The closest relationship was between BDQ222 and BDM221,and between BDQ222 and S26.SRAP markers have a high applicability in identifying plant types with close genetic relationship.By sequencing and analyzing polymorphic fragments,we speculate that some polymorphic fragments may be associated with variation of some traits of Jincheng.It will provide basis for future exploring Jincheng germplasm.