Chilli or pepper (Capsicum annuum, L.) is an imperative commercial crop developed solely in tropical and temperate zones of the world. Various pepper lines were developed from two different regions; China and Egypt have been studied for their diversity of total phenols, flavonoid content and antioxidants activity as well as its molecular genetic diversity using two different fingerprinting systems (RAPD and SCoT primers). The results showed that ethanolic extract (70%) of ILICA-256 and WAXY genotypes were contained a high level of total phenols (53.78 and 36.18 mg/g), respectively while ethanolic extract (70%) of genotypes ZUN-LA, P-70, ILICA-256, and WAXY were contained total flavonoids as follow,   0.43, 0.41, 0.37 and 0.36 mg/g, respectively and showed that highest value was recorded with genotype ZUN-LA. Antioxidant activity showed that P-70, ILICA-256, B-6, WAXY, and Z-1 extracts have a higher antioxidant activity against DPPH (21.49, 21.49, 18.86, 17.54 and 16.67%, respectively than that observed in R-15 and ZUN-LA as follow 12.72% and 13.77%, ferric reducing power results of the six lines ILICA-256, B-6, WAXY, P-70, Z-1 and ZUN-LA extracts had high mean values of FRAP  with values of 1.136, 1.072, 1.00, 0.99, 0.988 and 0.83, respectively than R-15 0.75 compared with TBHQ and quercetin. In molecular study six RAPD primers and five SCoT primers were used. RAPD-PCR analysis showed that studied lines are polymorphic in 47.61% while, SCoT markers scored polymorphism as 84.21%. Lines B-6 and ILICA-256 couldn't be distinguished with any specific markers while R-15 line was the most distinctive line that it characterized by the presence of five unique positive bands. P-70 was expressed by the presence of three positive unique bands and the absence of one band. ZUN-LA, Z-1, and WAXY were distinguished by one positive unique band for each. From pooled RAPD-SCOT data; the most two genetically related lines were ILICA-256 and WAXY while the most diverse line was R-15.