Abstract: The study was performed to explore the relationship between the setting percentages and the phylogenetic relationships. The purpose was to comprehend the influence factors of hybridization affinity among Paeonia suffruticosa. Sixteen Paeonia suffruticosa varieties were used as hybrid test materials, and using SRAP molecular markers to analysis the phylogenetic relationship between varieties. The results showed that: parents with a similarity coefficient of 0.31-0.35 tended to have a high setting percentage. The methods of parental selection in actual breeding work were suggested based on the present results. To get more hybrid seeds with purpose hybrid traits, so the parent should selected of a relatively farther hybridization.