Through observing twelve phenotypic traits and SSR genotyping result， this study analyzed 61 local pepper varieties and 39 offspring lines from the hybrids of 'Purple Color Pepper' and 'Red Pepper 809'. The results showed that twelve traits in the two populations of local pepper varieties and innovated pepper germplasm were significantly different （P≤0.05）， with the variation coefficient of the traits ranged from 1.15%-50.02% and 3.27%-60.67%， respectively， of which in local varieties vitamin C content was detected with the highest variations. The broad-sense heritabilities arranged from 79.24%-99.23% and 87.73%-98.80%， respectively， indicating that these traits were highly inheritable. Traits differentiation coefficients between the two populations arranged from 1.30% to 48.95%， of which anthocyanin content was the trait with the most obvious differentiation， while plant height had no obvious differentiation. Correlation analysis revealed 23 pairs of traits that were significantly or extremely significantly correlated. Comprehensive evaluation through principal component analysis identified 10 specific resources. In addition， 20 SSR markers identified 68 polymorphic bands， with the polymorphism ratio of 69.39%， and the higher polymorphic loci were detected in local varieties. Based on the clustering analysis of the twelve traits and molecular markers information， these germplasms were assigned to three groups， of which group I included most local varieties， and group II included most innovated germplasms， and group III contained 'PP1122' germplasm only. ‘PP1122’ showed large leaves， vigorous fruit， purple peel and high nutrient content. The hybridization of varieties between different groups， such as 'Purple colored pepper' and 'Red pepper 809'， was able to enlarge the genetic basis of pepper germplasm， providing a reference for pepper germplasm innovation and variety genetic improvements.