The geographical origin of watermelon (Citrullus lanatus) remains debated. While a first hypothesis suggests the center of origin to be West Africa, where the endemic sister species C. mucosospermus thrives, a second hypothesis suggests northeastern Africa where the white-fleshed Sudanese Kordophan melon is cultivated. In this study, we infer biogeographical and haplotype genealogy for C. lanatus, C. mucosospermus, C. amarus, and C. colocynthis using noncoding cpDNA sequences (trnT-trnL and ndhF-rpl32 regions) from a global collection of 135 accessions. In total, we identified 38 haplotypes in C. lanatus, C. mucosospermus, C. amarus, and C. colocynthis; of these, 21 were found in Africa and 17 appear endemic to the continent. The least diverse species was C. mucosospermus (5 haplotypes) and the most diverse was C. colocynthis (16 haplotypes). Some haplotypes of C. mucosospermus were nearly exclusive to West Africa, and C. lanatus and C. mucosospermus shared haplotypes that were distinct from those of both C. amarus and C. colocynthis. The results support previous findings that revealed C. mucosospermus to be the closest relative to C. lanatus (including subsp. cordophanus). West Africa, as a center of endemism of C. mucosospermus, is an area of interest in the search of the origin of C. lanatus. This calls for further historical and phylogeographical investigations and wider collection of samples in West and northeastern Africa.
