Abstract: Extracts of different genotypes of Capsicum (C. annuum L., C. baccatum L., C. chinense Jacq., C. frutescens L. and C. praetermissum) were investigated for total phenolics, flavonoids, capsaicinoids contents and antioxidant activity objectifying to determine the relations between these bioactive compounds and the antioxidant capacity and also examine its cytotoxic and genotoxic potential. Capsicum praetermissum showed the highest total antioxidant activity and the highest concentrations of phenolic compounds and flavonoids. For C. annuum and C. frutescens the antioxidant activity was significant and the levels of phenolic compounds and flavonoids intermediate, while C. baccatum demonstrated the lowest antioxidant activity independent of significant levels of these compounds. Capsicum chinense showed the lowest level of total phenols and flavonoids despite expressive antioxidant activity. The determination of capsaicinoid content revealed higher levels of capsaicin and dihydrocapsaicin for extracts of C. praetermissum, intermediate levels to C. baccatum, C. chinense and C. frutescens, whereas, the C. annuum showed the lowest levels of capsaicinoids, typical of these ornamental genotype. The extracts of C. praetermissum and C. baccatum exhibited low cytotoxic potential compared to other genotypes. The genotoxic potential was variable between analyzed genotypes, with C. praetermissum presenting the lowest rates. All species showed a dose-effect relationship dependent of extract concentration. The results of the present study indicated that Capsicum genotypes demonstrated a very high diversity of bioactive compounds that can be explored as agents in the control of complex biological processes related to human nutrition and health.