AFLP technique was used to elucidate systematic relationships among 26 cultivars of Tree Peony. Six AFLP primer combinations (M+3 and P+3) were used to produce recognizable 757 bands, among which 623 bands are polymorphic. The percentage of polymorphic bands was 82%, suggesting abundant genetic diversity among sect. Moutan. Clustering analysis showed that some cultivars of dwarf and tall peony types clustered separately, the cultivars of the same follower former only clustered partially. The clustering result based on DNA bands among the cultivars was not consistent with that based on the plant highness and flower former.