Background: The trees Prunus armeniaca (apricot), P. mume (mei or Chinese plum), and Armeniaca mume (xingmei) are all members of the Armeniaca section of the genus Prunus. The three trees are cultivated widely in China. Hypotheses: Geographical distribution and divergent flowering phenologies constitute pre-zygotic, reproductive isolation barriers that promoted the speciation of P. armeniaca and P. mume. Xingmei is an artificial hybrid of the other two species. Methods: We studied the geographic distribution and flowering phenologies of armeniaca and P. mume cultivars from different regions of China. We analysed the copious data of the China Fruit Records (mei and apricot). To examine the origin of xingmei, we analysed the F-2 progenies of P. armeniaca x P. intone using a species-specific molecular marker. Finally, we researched the genotypes of P. mume, P. armeniaca, and xingmei to determine whether the three are post-zygotically isolated. Results: Isolation due to geographical location and flowering phenology are strong pre-zygotic isolation barriers that maintain the separation of P. armeniaca and P. mume. That separation limits the opportunity for natural hybridization between these two species, and probably prevented the natural appearance of xingmei. Furthermore, no post-zygotic reproductive isolation exists between P. armeniaca and P. mume. Conclusions: Pre-zygotic isolation played an important role in the evolution of P. armeniaca and P. mume. It prevented their natural hybridization. Xingmei is likely to be an artificial hybrid.