Abstract: The study of the phylogenetic relationship was carried out with ISSR molecular markers among Shuanla（Capsicum frutescens L. var. shuanlaense）and other five cultivated Capsicum species （Capsicum annuum，C. frutescens，C. chinense，C. baccatum and C. pubescens）including 71 pieces of
germplasm in total. Genomic DNA was amplified with 11 screened ISSR primers by PCR，a total of 112 polymorphic bands were amplified，polymorphism bands reached 90.17% in average. Genetic similarity coefficient of all material located between 0.049 and 0.875. At the point of the similarity coefficient 0.31，
C. frutescens var. shuanlaense and C. frutescens which originate in USA was classified in a group，which proved C. frutescens var. shuanlaense belonged to C. frutescens with molecular measure. C. frutescens var. shuanlaense had the closest relationship with C. annuum，followed by C. chinense，and C. baccatum more distantly related，the relationship with C. pubescens is the most distant. At the point of similarity coefficient 0.397，66 pieces of germplasm belong to C. annuum were further classified into 7 subgroups，Gejiu Wrinkled Pepper and Jianshui Yingtaojiao（C. annuum var. cerasiforme）were separated into two subgroups. The rest were var. longum，var. dactylus + var. breviconoideum，var. grossum，var. cerasiforme and var. fascicutatum. Basically they are consistent with the pepper morphological classification results.

Key words: Capsicum, genetic diversity, ISSR, cluster analysis