The relationship between papaya (Carica papaya) and its closest relatives, the mountain papayas (Yasconcellea spp.), was studied by PCR-RFLP analysis of three non-coding cpDNA regions (trnK3-trnK4, trnC9-trnD10. and trnD11-trnT12). The sample included eight accessions of C papaya and 54 accessions from 12 species of Vasconcellea. A high polymorphism was observed, even at the intraspecific level, with 42 different haplotypes. The neighbor joining cluster analysis and the principal coordinate analysis showed important distances between the two genera as well as within Vasconcellea. The Vasconcellea species most represented in the sample, V. cundinamarcensis, displayed a particularly wide variation. In this and other Vasconcellea species, a few accessions clustered with distinct species, suggesting chloroplast haplotype capture and a reticulate evolution in the genus. Two of the eight accessions of V. stipulate appeared closely related to V. x heilbornii, while the six others appeared more distant than such species as V. weberbaueri and V. parviflora, indicating that V. x heilbornii may have derived from a particular lineage of V. stipulata. Within V. x heilbornii (babaco and baby-babacos), variation was comparable to that of other species, which does not support a recent hybrid origin of these cultigens.