The genus Prunus contains the subgenus Prunus incorporating the European plums (section Prunus), the North American plums (section Prunocerasus) and the apricots (section Armeniaca). In section Prunus, there are approximately 20 species, which occur in three levels of ploidy, diploid 2nDespite a clear distinction between section Prunus and the other sections, phylogenetic relationships between species within the section are unclear. We performed a phylogenetic analysis on members of the section Prunus and three outgroup species using sequence data from four single-copy phylogenetically informative chloroplast DNA regions (atpB-rbcL, matK, rpl16, and trnL-trnF). After alignment, the analysed regions totalled 4,696 bp of sequence, containing 68 parsimonyinformative sites and 14 parsimony-informative indels. Data were analysed using both maximum parsimony and Bayesian likelihood and phylogenetic trees were reconstructed. The analyses recovered trees with congruent topologies and similar levels of statistical support for relationships between taxa. They confirmed that species belonging to section Prunus form a monophyletic clade within Prunus. The section is resolved into four wellsupported clades, which correspond to the geographical distribution of the species. The hexaploid species could not be resolved into distinct species clades but formed a wellsupported group separate from the tetraploid species, highlighting the distinct evolutionary origins of the different polyploid groups. The close relationship between the hexaploids and Prunus divaricata, Prunus cerasifera and Prunus ursina indicates the former may have derived from an ancestor of P. cerasifera and its allies.