Passion fruit is an important crop in Brazil, therefore the study of its wild species is necessary to expand the passion flora genetic basis. This can be done by using the biotechnology that has enhanced the use of markers in improvement programs. During the germplasm characterization, molecular markers show different use complementing the morphological and agronomic information. This study aimed to characterize and to quantify the intra and interspecific genetic variability of Passiflora spp. accessions, using ISSR and RAPD molecular markers. 146 ISSR and 271 RAPD markers were obtained. They were used to estimate genetic dissimilarities among the accessions. The genetic dissimilarity matrices were used to perform cluster analysis by dendrogram using the Unweighted Pair-Group Method as grouping criterion and by graphic dispersion based on multidimensional scaling, using the principal coordinates method. There was a significant correlation of 0.56 between the genetic distances estimated based on ISSR and RAPD markers. The molecular markers characterization showed high genetic variability and adequate accessions differentiation. There was a clustering tendency of accessions and hybrids of the same species.
