Secondary metabolites of Capsicum spp. have biological activity, which can be modified by external factors as the amount of incident light and soil water availability during crop growing, and by internal factors as fruit ripeness level. The study aim was to determine by HPLC method the phytochemical profile of C. annuum L. var. glabriusculum (Dunal) Heiser & Pickersgill (AMA and GAR genotypes) and C. frutescens L. (PIP genotype) grown under open sky and 70% shade during dry and rainy harvest season. Phytochemicals were affected by genotype, light level, harvest season, and fruit ripeness level. Phytochemicals number changed among genotypes: PIP > AMA> GAR. In immature fruits AMA (4.74 mg g -1 ) and GAR (3.83 mg g -1 ) had highest capsaicin content; and PIP (0.43 g g -1 ), AMA (0.18 g g -1 ) and GAR (0.14 g g -1 ) in lutein content in all harvest seasons and light level conditions studied. In mature fruits, PIP had the highest capsaicin (5.77 mg g -1 ) and β-carotene (0.45 g g -1 ) content. Gallic and syringic acids were major constituents of phenolics acids, and quercetin and rutin for flavonoids. Mature and immature fruits from 70% shade showed the quercetin highest content (108.4-160.02 g g -1 ), increasing during dry season (180.9-1368.6 g g -1 ). Gallic acid (789.3-1076.7 g g -1 ) and rutin (114.0 g g -1 ) increased in AMA immature fruits when grown under open sky. Ferulic acid was not detected in GAR under any of the conditions studied. In AMA, ferulic, protocatechuic and p-hydroxybenzoic acids were detected only in rainy season fruits in both light levels. The harvest season and shading level of these Capsicum spp. should be considered when evaluating the biological activity of chili peppers fruits extracts in tropical crops.