Morphological characteristics of pequi fruits (Caryocar brasiliense) allows us to obtain information for the conservation, breeding, and detect genetic variability. Thus, the aims of this research were to characterize the genetic diversity of Caryocar brasiliense that produce fruits with and without thorn at the endocarp; determine the important characters in the study of genetic diversity, and to estimate phenotypic and genotypic correlations. 80 fruits with thorns and 90 fruits without thorns were evaluated. Data were used for analysis: Euclidian distance as a measure of dissimilarity and the Tocher method for delimitation of groups; Principal Component Analysis, and genotypic and phenotypic correlations. Genetic dissimilarity of C. brasiliense ranged from 0.066 (B6-D6) to 0.908 (A14-B3). Tocher method allowed dividing the matrices into three groups, the dendrogram into five groups, and the principal components allowed the distribution in 8 groups. We observed 15 significant correlations for characters of fruit with thorns and 31 correlations for characters of fruit without thorns. The weight of the fruit (with thorns) and the pyrene yield (without thorns) are relevant correlations for production. The groupings generated allowed the classification of the matrices into distinct sets. Allowed the identification of potential producers plants that could be used in breeding programs.