In order to reveal the genetic diversity of the backbone parents in pepper breeding in Jiangxi province， as well as decipher their DNA fingerprints， capillary electrophoresis and SSR molecular marker techniques were applied to analyze 60 pepper germplasms from Jiangxi province. The results showed that a total of 202 alleles were detected via 49 pairs of SSR primers， with an average of 4.122 alleles from each pair of primers and an average of 2.172 effective alleles. The mean value of Shannon’s information index was 0.850， and the polymorphism information content （PIC） was 0.414， indicating that the tested materials had abundant genetic diversity. The expected heterozygosity （0.475） was averagely greater than the observed heterozygosity （0.126）， indicating that the homozygosity of the tested materials was high through continuous selfing for multi-generations. The clustering analysis， population structure analysis and principal coordinate analysis （PCoA） were used to classify the tested materials， and the 60 germplasms were separated into three sets， two populations and three groups， respectively. The consistency of results from different clustering methods supported that the founder parents of pepper breeding in Jiangxi province were mainly from the southern China region and germplasms of small-fruit-type， with narrow genetic origination and relatively simple kinship. In addition， PM1， CAMS-855， CO911525S， PM22， HpmsE015 and Hpms1214 were identified as the core primers based on multi-loci matching analysis. Meanwhile， DNA fingerprints of the 60 pepper germplasms were deciphered by using the six core primers. This study provides a reliable basis for the characterization and protection of pepper resources， and for the selection of optimal parents in molecular assisted breeding.