We investigated the origins of the sickle allele by using whole-genome-sequence data from a total of 2,932 individuals from the 1000 Genomes Project, the African Genome Variation Project, and Qatar. We identified a total of 156 sickle carriers. We classified haplotypes by using phased sequence data comprising diallelic sites (both single-nucleotide polymorphisms and short insertions or deletions). We then used a combination of forward time simulation, phylogenetic network analysis, and coalescent analysis to infer a single origin of the sickle allele approximately 7,300 years ago, during the Holocene Wet Phase or Green Sahara.