Background <p>The <i>Passiflora</i> genus presents a representative variability of passion fruit species with food, pharmacological and ornamental potential. To understand this genetic variability, it is essential that genetic resources are well characterized for future use in breeding and conservation programs. The aim of this study was to investigate for the first time the diversity genetic and structure population of 88 <i>Passiflora</i> genotypes with the use of inter-primer binding site (iPBS) markers.</p> Methods and results <p>Genotypes were grouped through Unweighted Pair-Group Mean Average (UPGMA). The population structure analysis was carried out by two methods using model-based Structure analysis and cluster-based discriminant analysis of principal components (DAPC). Samples of 88 genotypes were analyzed using 24 iPBS markers, of which 19 of them generated 234 informative bands, with an average of 12.32 per locus, ranging from 5 to 18 alleles. Polymorphic information content (PIC) values varied between 0.14 and 0.43, with an average value of 0.28. Nei’s genetic diversity (<i>He</i>) as 0.28 and Shannon’s information index (<i>I</i>) as 0.43. The genetic dissimarity for the 88 <i>Passiflora</i> genotypes ranged from 0.11 to 0.97, with mean values of 0.74, indicating substantial genetic diversity. Molecular variance analysis (AMOVA) indicated that within group variations contributed more (51%) to the genetic diversity than among group variations (49%), with percetage of the genetic differentiation coefficient (<i>F</i>_<i>ST</i>= 0.49). Discriminant analysis of principal components (DAPC) corroborated by cluster analysis (UPGMA) and Bayesian model-based analysis of population genetic structure categorized all materials into ten groups. Notably, a substantial portion of genotypes clustered within populations correlated with the <i>Passiflora</i> species. The ornamental hybrids were all discriminated based on the iPBS markers used and the G9 group allowed for the allocation of at least six of them.</p> Conclusions <p>The results of this study provide valuable information for passion fruit germplasm management and contribute to the improvement of current breeding strategies. They also demonstrated the effectiveness of iPBS retrotransposon markers in detecting genetic differentiation and reliably elucidating genetic relationships among passion fruit genotypes, thereby supporting breeding programs and germplasm conservation efforts.</p>