12 traits and SSR molecular marker information of genomic DNA of local pepper varieties and innovative pepper germplasm were observed in the experiment, and genetic correlation analysis and diversity evaluation were conducted. The results show that: 12 traits in the two populations of local pepper varieties and innovative pepper germplasm were significantly different(P≦0.05), and the variation coefficient of the traits ranged from 1.15%－50.02% and 3.27%－60.67% respectively, with the local varieties of vitamin C showing the highest variations; The broad-sense heritabilities were in the ranges of 87.73%－98.80% and 79.24%－99.23% respectively, indicating that the traits were mainly determined by genetics; Traits differentiation coefficients between the two populations were in the range of 1.30%－48.95% respectively, of which anthocyanin content was the trait with obvious differentiation, while plant height had no obvious differentiation; 22 reached the level of significant correlation between the traits (P≦0.05); 10 specific resources were screened out by principal components. 20 effective primer pairs of SSRs were selected, and the PCR amplification identified 68 polymorphic loci, the polymorphism ratio was 69.39%, with the polymorphic loci of local varieties in the majority. However, one specific locus in innovated germplasm ' PP1122 ', and genotyping and genetic polymorphism evaluation were performed according to molecular markers. Based on the clustering analysis of the 12 traits and molecular markers information, germplasm for test can be divided into three groups, local varieties clustered in group I, innovative germplasm clustered in group II, and group III, only contained 'PP1122' germplasm, which had large leaves, vigorous fruit, purple peel and high nutrient content, and indicates that the innovative germplasm has a relatively distant relationship with local varieties, The hybridization of different groups of varieties such as 'Purple colored pepper' and 'Red pepper 809' was beneficial to expand the genetic background of pepper germplasm. This study provides a for pepper germplasm innovation and a variety of genetic improvements.