Phylogeny of Prunus was reconstructed by maximum parsimony analysis of three markers, ITS, s6pdh and the chloroplast spacer trnL-trnF. Over forty species from all subgenera and most sections of Prunus were included in the analyses of ITS and trnL-trnF. ITS provided more informative sites but was highly homoplastic, whereas trnL-trnF was less variable and showed little homoplasy. Combined analysis of these two markers separated Prunus into two groups; a well supported Cerasus /Padus /Laurocerasus clade and a second group that contained the rest of Prunus. The data suggest a Eurasian origin for Prunus with multiple radiations into North America. A subset of the samples were selected for phylogeny reconstruction using s6pdh, a nuclear gene encoding an enzyme involved in sorbitol metabolism. Fourteen species of Prunus, representing all major clades found by the previous study using ITS and trnL-trnF, were included. Maximum parsimony analysis of s6pdh sequences agrees with results obtained with ITS and trnL-trnF. Some changes in the classification of Prunus are necessary. For example it is evident that section Microcerasus, previously placed in subgenus Cerasus, is actually more closely related to subgenus Prunus. Evolution of morphological traits such as dry fruits, and their ecological significance are discussed

Key words: ITS, phylogenetics, Prunus, s6pdh, trnL-trnF