The fruit woodiness disease induced by the cowpea aphid-borne mosaic virus (CABMV) is considered to be of the greatest economic importance in the Passiflora crop. There are no reports of resistance to CABMV identified in P. edulis, and none of the Passiflora cultivars registered thus far are resistant to the virus. On this basis, breeding programs have resorted to wild species to identify sources of resistance that can be efficiently transferred to the cultivated species via interspecific crossing. A preliminary map for a segregating population of Passiflora based on seven microsatellite markers and 43 inter-simple sequence repeat markers was constructed using a BC1 population composed of 187 individuals. The map was generated using JoinMap software and the linkage groups were formed and ranked using a lod score of 3.0 and a maximum recombination value of 40%. The linkage map consisted of 50 markers - 43 ISSR and seven SSR. The generated map covered 1017.1 cM, with one larger linkage group of 211.2 cM and eight smaller groups ranging from 1.8-179.3 cM. Each linkage group contained 3-12 markers, with one marker occurring at every 20.34 cM. Of the total markers, 55% were mapped, and 40.68% of the Passiflora map was covered. Seven small-effect QTL were detected for resistance to CABMV in seven linkage groups. The phenotypic variation rate ranged from 1.45 to 4.68%, totaling 21.81%. This is the first report involving QTL mapping for resistance to CABMV in a segregating population of Passiflora obtained from interspecific crossing.