Abstract:EST-SSR is a molecular marker based on functional genomics, had been widely used because of its evenly distributed among the genome, better universality between species or genera and characters associated with the phenotypic traits. We downloaded the EST sequences of six genera in Rosaceae (Rosa, Malus, Pyrus, Prunus, Fragaria and Rubus) to study the distributed characteristic of SSR in Rosaceae by bioinformatics methods. There was significant difference of EST-SSR distribution frequency among genera, from 10.94%(Rubus) to 43.49%(Pyrus). The dinucleotide and trinucleotide repeats were the major types, AG/CT, GA/TC and AT/TA were the preponderant dinucleotide motifs, the trinucleotide repeats showed significant difference among genera, and the dominant type included AGA/TCT, GAA/TTC, AAG/CTT, CAC/GTG and ACA/TGT. Our results provided a research platform for plant molecular phylogeny and evolution, germplasm identification, genetic diversity and genetic mapping of Rosaceae.