ABSTRACT. Genetic diversity and structure were analyzed in 10 accessions belonging to Banco Ativo de Germoplasma de Capsicum located at Federal University of Piauí in northwestern Brazil that receives pepper samples grown in community gardens in various regions and Brazilian states. Selections were made from seeds of C. chinense (4 accessions), C. annuum (5 accessions), and C. baccatum (1 accession). Samples consisting of leaves were collected from 4-10 plants of each accession (a total of 85 plants). Native polyacrylamide gel electrophoresis was used to identify α-and β-esterase polymorphisms. Polymorphism was clearly detected in 5 loci. Sixteen alleles were found at 5 α/β-esterase loci of the three Capsicum species. In the C. chinense samples, the highest H O and H E values were 0.3625 and 0.4395, respectively, whereas in C. annuum samples, H O and H E values were 0.2980 and 0.3310, respectively; the estimated H O and H E values in C. chinense samples were higher than those detected in C. annuum samples. A deficit of homozygous individuals was found in C. chinense (F IS = -0.6978) and C. annuum (F IS = 0.7750). Genetic differentiation between C. chinense and C. annuum at these loci was high (F ST = 0.1867) indicating that C. chinense and C. annuum are genetically structured species for α/β-esterase isozymes. The esterase analysis showed high genetic diversity among the C. chinense and C. annuum samples and very high genetic differentiation (F ST = 0.6321) among the C. chinense and C. annuum samples and the C. baccatum accession.