Genetic relations between the main cultivated passion fruits, as well as ,two of their wild relatives, were studied with AFLP markers. The 28-accession sample included six species from subgenus Passiflora (P. edulis, P. alata, P. quadrangularis, P. ligularis, P. tiliifolia, P. maliformis) and five from subgenus Tacsonia (P. tripartita, P. tarminiana, P. cumbalensis, P. mixta, P. antioquiensis). Three pairs of primers were selected on the basis of number and quality of polymorphic fragments. A total of 314 informative fragments were identified in the 80-500 bp range, 58% of them showing polymorphism. The neighbor joining cluster analysis grouped the accessions by species, and botanical varieties (P. tripartita) or forms (P. edulis). P. edulis displayed considerable variation, with a clear separation between its purple and yellow forms. The separation between the two subgenera was poor. At the intermediate series level, P. alata and P. quadrangularis were logically associated in a Quadrangulares branch, as well as P. ligularis and P. tiliifoliae in a Tiliifoliae branch. However, P. maliformis appeared independent from the latter. AFLP markers confirmed their interesting potential to study genetic diversity at the intraspecific level and among closely related species.