Ornamental pepper plants have genetic variability, which can be accessed through morphological and molecular traits. Genotype selection to form the base population for breeding can be performed through the joint analysis of several types of data, providing greater selection accuracy. From this perspective, this study aimed to evaluate the diversity among pepper accessions based on analysis of phenotypic traits and molecular markers and to select the best ones to use as parents in breeding programs. The study was carried out at the Centro de Ciências Agrárias of the Universidade Federal da Paraíba, Paraíba, Brazil. Sixteen ornamental pepper genotypes were used and characterized for eight quantitative traits, nine qualitative traits, and 18 pairs of microsatellite primers. Simultaneous variable analyses were performed using Tocher’s clustering method, Ward’s clustering algorithm, and the dissimilarity matrix. The clustering methods were efficient in separating the genotypes, identifying genetic variability, and accuracy in the selection through the joint analysis of quantitative, qualitative, and molecular data. Different groups were formed among the genotypes by Tocher’s method (six groups) and Ward’s method (three groups). There is genetic variability among ornamental pepper genotypes considering the joint analysis of quantitative, qualitative, and molecular data. Qualitative traits are important in the identification of genetic divergence among ornamental pepper accessions. The UFPB genotypes 46, 134, 137, 443 and 449, the mini pepper Akamu, and the cultivar Calypso are indicated for selection and can be used to carry out crosses and continue the breeding program.
