Abstract Capsicum is one of the most important genera of the Solanaceae family. Among the domesticated species, C. chinense is considered the most Brazilian pepper, besides being known for having high levels of phytochemical compounds and, consequently, high antioxidant capacity. This work was intended to perform the chemical characterization of bioactive compounds present in C. chinense accessions from the Capsicum Genebank of Embrapa Temperate Agriculture. Fruits from 19 accessions were evaluated regarding the concentration of total phenolic compounds, total carotenoids, total anthocyanins and antioxidant activity. It was possible to observe a high genetic variability among the evaluated accessions. The highest concentration of phenolic compounds was found in accession number P391; the highest concentrations of total carotenoids were found in accession numbers P240; P348 and P399; the highest concentration of total anthocyanins was in accession number P240; and the highest antioxidant activity was found in accession numbers P386, P391, P366, P350, P346 and P399. There is a correlation between antioxidant activity and the content of phenolic compounds, as well as between antioxidant activity and carotenoids in Capsicum chinense. The genetic variability noticed can be exploited in breeding programs for the selection of accessions with desirable characters.