Catha edulis (Vahl) Forssk. ex Endl. (qat, khat, mirra) is a woody plant species that is grown and consumed in East Africa and the southern Arabian Peninsula for its stimulant alkaloids. The alkaloids responsible for the stimulant properties are cathinone, cathine, and norephedrine. These alkaloids are structurally and pharmalogically similar to amphetamines. The evolution of these alkaloids across the Celastraceae family has not been examined, yet ethnobotanical accounts indicate that other closely related species are used as stimulants much like qat. Using methods from analytical chemistry we found that the alkaloids in qat are unique to that taxon. However other Celastraceae species were found to be enriched in unique compounds such as alkaloids, sterols, terpenes, sesquiterpenes and triterpenes that may account for their stimulant properties. The origin and timing of qat cultivation has been argued in the ethnobotanical and historical literature with the mountainous areas of Ethiopia, Kenya, and Yemen being the most often mentioned as the places of origin for cultivated qat. The time period in which qat was initial cultivated has not been robustly tested with molecular data, but rather asserted through conflicting historical documentation. Despite the uncertainty in dating the initial cultivation event(s) for qat, it is known that qat is a relatively recent domesticate compared to other clonal crops like grape, banana, or apple. Due to the recent initial cultivation of qat, heretofore unknown insight into the rate and type (somatic and allele-frequency changes) of evolution at the early stages of domestication can be determined—a comparison not possible among more ancient clonal crops. With over 1500 samples from across the native range of qat, including sampling areas of commercial production, and 19 SSR loci, qat cultivation was found to have two centers of origin—in Ethiopia and Kenya. Using Bayesian coalescent simulations the scenario in which the Ethiopian origin of cultivation predates the Kenyan origin had the strongest support. From the initial results the rate of SSR evolution was calculated between wild populations and from wild populations to cultivated and found to be higher among cultivated populations compared to wild populations.