The carnauba palm Copernicia prunifera is the third most important non-timber forest species in Brazil; it is mainly known for the production of carnauba wax. We examined intrapopulation genetic diversity and correlated genotypic and phenotypic traits of 28 trees from a coastal location in Rio Grande do Norte state. Phenotypic variables tree height, diameter at breast height, curvature of the stem, fresh mass of fruits and seeds, and length and diameter of fruits and seeds were evaluated. Genotypic parameters were examined based on inter-simple sequence repeat (ISSR) polymorphisms. The eight ISSR primers detected 79 loci, of which 76% were polymorphic. The polymorphic information content ranged between 0.408 and 0.500, the Nei's diversity index h was 0.327, and Shannon index was 0.470. Although there was no significant association between the matrices of genotypic and phenotypic traits, stepwise multiple regression analysis identified ISSR markers that can be used in a marker-assisted breeding program. The ISSR loci 881(2), 880(1), and M1(4) were significantly and positively associated with plant height. The sMRA also identified a positive association between DBH and 842(5) and a negative association between the curvature of the stem and 857(1). The fresh mass of fruits had a significant negative correlation with ISSR locus 840(1). The other traits showed positive and negative associations when the marker(s) of the previous step(s) were included in the succeeding step in sMRA analyses. These results are relevant for breeding programs, with the perspective of obtaining intra specific hybrids that are superior for desirable characters.