Cladistic analysis of 86 chloroplast DNA restriction-site mutations among 30 samples representing 15 species of Cucurbita indicates that annual species of the genus are derived from perennials. The Malabar Gourd, C. ficifolia, is placed as a basal, sister taxon relative to other domesticated species and allied wild-types. The pattern of variation supports three species groups as monophyletic: (1) C. fraterna, C. pepo, and C. texana, (2) C. lundelliana, C. martinezii, C. mixta, C. moschata and C. sororia, and (3) C. foetidissima and C. pedatifolia. Domesticated samples representing subspecies of C. pepo are divided into two concordant groups, one of which is allied to wild-types referable to C. texana and C. fraterna. The data failed to resolve relationships among cultivars of C. moschata and C. mixta and their association to the wild C. sororia. The South American domesticate, C. maxima, and its companion weed, C. andreana, show close affinity and alliance to C. equadorensis.