The two major species of cherries in world trade are the diploid Prunus avium L. (sweet cherries) and the tetraploid Prunus cerasus L. (sour cherries). The sour cherry is an allopolyploid species, probably as a result from a natural hybridization between ground cherry, P. fruticosa, and unreduced pollen of the sweet cherry, P. avium. In rootstock breeding, major species include P. avium, P. cerasus, P. canescens Bois, P. fruticosa Pall., and P. mahaleb L. Sweet cherries are divided into four groups based on fruit color, shape, and texture: black geans, amber geans, hearts, and bigarreaux, whereas sour cherries are divided into two groups: Morellos (Griottes, Weichsel) with red to dark red colored juice and Amarelles (Kentish) with colorless juice. It has been suggested that sweet cherry originated in an area south of the Caucasian mountains with a secondary dissemination into Europe. The sour cherry, Prunus cerasus L., is native from middle and south Europe to north India, Iran, and Kurdistan, and its center of origin extends from the south border of the Black Sea along Anatolia and the south Caucasus to Iran. Major breeding objectives are fruit size, firmness, fruit quality, self-fertility, extended harvest season, and adaptability to mechanical harvest. Recently, precocity, and productivity, resistance to rain-induced cracking, resistance to diseases and insects are additional goals. Breeding for rootstocks are focused in the effect of the rootstock on the scion in traits as vigor, growth habit, precocity, and fruit quality. Graft compatibility and good propagation for nurseries are important questions along with pest resistance and adaptability to soil and environmental conditions. Genetic linkage maps are being developed for sour cherry. There is a growing body of work in other Prunus species, particularly peach and almond, that have great potential for application to cherry. Transformation protocols have been applied to sour cherry, but sweet cherry has been proven very difficult to transform.