Passiflora cincinnata Mast. is a wild passion fruit species widely distributed in Brazil, with diverse economic potential and source of resistance to biotic and abiotic stress factors. Despite this, molecular genetic studies on this species are incipient, which limits the definition of priority regions for conservation and identification of accessions to be prospected for germplasm banks and inserted in genetic improvement programs. Thus, this study aimed to characterize the structure and genetic diversity of P. cincinnata accessions using inter simple sequence repeat (ISSR) markers. The study was carried out using leaf samples from 213 accessions of P. cincinnata, with 158 accessions from six natural populations (collectively considered in this study as a hypothetical metapopulation) in the state of Bahia, Brazil, and the other 55 accessions from two collections of Embrapa Cerrados and Embrapa Cassava & Fruits active germplasm banks (AGBs). Genetic estimates were based on an analysis of the amplification profile of 12 ISSR primers. Descriptive statistics analysis and the polymorphic information content (PIC) and expected heterozygosity (He) estimates were carried out using the GENES software. Approaches based on the Bayesian model, principal coordinate analysis (PCoA), and analysis of molecular variance (AMOVA) were used to assess the genetic structure. Passiflora cincinnata populations/collections showed high polymorphism rates. The metapopulation showed 25.3% of private markers/alleles. The metapopulation is structured in at least three genetic groups, while AGBs in two genetic groups. AMOVA indicated higher diversity within populations, with low differentiation between them.