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The genus Capsicum has 27 species, being five domesticated and 22 semi-domesticated and wild ones. For an enhanced use of the germplasm in breeding programs it is necessary to know the accessions in the collections, to identify them and evaluate the genetic diversity. Objectives of this research were to quantify the genetic diversity among 70 Capsicum accessions, confirm their identification and verified possible duplicated accessions, using RAPD markers. Results showed that there is genetic diversity within and among species and were in agreement with botanical and morpho-agronomic classifications. The identification of 53 accessions was confirmed (16 C. annuum, 7 C. frutescens, 14 C. baccatum and 16 C. chinense) and among botanically non-identified accessions results suggested that six belong to C. baccatum and five to C. chinense. The most distinct accession was UENF 1620, probably a wild species that is not represented in the collection yet.