Abstract: To analyze the molecular evolution and phylogeny of stone fruit trees，the internal transcribed spacers（ITS）of nuclear ribosomal DNA isolated from 16 genotypes of peach（Prunus persica），plum（P. salicina），apricot（P. armeniaca），mei（Prunus mume），and cherry（Prunus avium），2–4 genotypes per species，were sequenced. All these ITS sequences together with other 6 ones downloaded from the GenBank were analyzed using the second way of rooting with cherry used as the root. The broad data set was tested with 56 evolution models by PAUP 4.08b software，and the scores were used to screen the best model and parameters with Modeltest 3.7 software. Mega 3.1 software was used to calculate genetic distance and variance among the genotypes and to construct maximum parsimony phylogenetic tree. The result indicated: Molecular evolution rates of ITS1 and ITS2 among the stone fruit trees were different，same did the information of them; the evolution order of 5 stone fruit trees was that cherry，plum，and apricot originated from same one ancestry plant，and then plum evolved to peach and apricot to mei；Prunus mandshurica is more original than P. sibirica and P. armeniaca；the evolution order in Prunus persica is from P. andersonii to P. davidiana and then to P. persica，P. ferganensis. It is reasonable that stone fruit trees are divided into 4 subgenera.

Key words: stone fruit trees, phylogeny, ITS, molecular evolution