DNA variation was studied at the intra- and interspecific levels within the genus Passiflora, with particular emphasis on the subgenus Tacsonia and its relationship with the subgenus Passiflora. AFLP fingerprints were generated for 35 accessions from 21 species, 14 of which belong to subgenus Tacsonia, and four to subgenus Passiflora. The morphologically intermediate P. manicata (subgenus Manicata) was also included, as were P. trinervia (subgenus Psylanthus) and P. alnifolia (subgenus Decaloba). The two latter were used as outgroup species. Two primer combinations generated 34-80 scorable fragments per genotype for a total of 260 fragments. Polymorphism analyses spanned the levels from individual genotype to section. Subgenus Tacsonia presented wide genetic variability at both intra- and interspecific levels, particularly within wild species. The classification based on these markers generally agrees well with current taxonomic definitions of common species, but less with definitions of sections. A geographical component was evident in the intraspecific variation of P. mixta, P. tripartita var. mollissima and P. tarminiana, with wider variation in Ecuador and Peru than in Colombia and Venezuela. These same three species. plus P. cumbalensis, formed adjacent clusters, showing closer affinity with each other than with the other species of subgenus Tacsonia. As expected, P. manicata clustered at an intermediate position between subgenera Tacsonia and Passiflora.