This study investgated the genetic diversity of Capsicum frutescens germplasm of Guizhou region in the southwest of China,provide accurate reference for the conservation,utilization and molecular marker assisted selection of Capsicum frutescens germplasm.20 SSR molecular markers were used to analyze genetic diversity of 112 Capsicum frutescens germplasm resources in the southwest of China.The results showed that 20 pairs of SSR primers amplified 65 polymorphic bands,with 2—4 loci amplified by each pair of primers,the average of effective number of alleles was 1.829 4,the average of polymorphism information content(PIC)was 0.544 0,the average of Shannon’s information index(I) was 0.723 4,the mean values of observed heterozygosity(Ho),expected heterozygosity(He),Nei’s expected heterozygosity were 0.492 0,0.433 7 and 0.431 8 respectively.The 20 pairs of SSR primers were highly polymorphic and could reflect the genetic diversity information among different local varieties of Capsicum frutescens.The clustering results showed that the genetic similarity coefficient(GS)value of the material population ranged from 0.569 2 to 0.953 8,and the average of GS was 0.773 3,indicating that the genetic similarity between Capsicum frutescens local varieties was relatively high and the genetic relationship between the materials was relatively close.The materials clustered into 4 branches at GS value of 0.767 0.The clustering results showed that the overall distribution of 112 Capsicum frutescens materials was related to the geographical distribution,but there was also inter regional and inter provincial infiltration,and each category gathered materials from different geographical sources.