Abstract: In order to provide a genetic basis for studies on complex quantitative traits and for molecular marker assisted breeding of tree peony, the genetic diversity of Paeonia rockii was determined by using SSR markers and their association with important ornamental traits was detected. A total of 11 simple sequence repeat (SSR) markers were screened for polymorphism among 99 accessions, and then the genetic diversity of these materials was detected. Through analyzing population structure, association analysis between SSR markers and 32 horticultural traits were performed using TASSEL2.1 GLM (general linear model) programs. The results showed that a total of 94 alleles were identified with 8.5 alleles per locus. The polymorphism information content (PIC) value ranged from 0.146 to 0.850, with an average of 0.593. The genetic diversity ranged from 0.152 to 0.862, with the mean of 0.630. Population structure analysis showed that 99 Paeonia rockii materials were composed of 3 subpopulations. Association analysis found that there were 5 SSR markers associated with 6 horticultural traits, and the rate of explanation on the phenotype of related marker ranged from 30.4% to 55.8%. Among them, FJ024285 and FJ024294 were associated with plant height; FE528073 was associated with top-leaf length, stigma color and disk color; FJ024287 was associated with length ratio of petiole and compound leaf; EU678295 was associated with blotch size. An abundant genetic variation but week population structure was detected in Paeonia rockii accessions, indicating that the association population is representative and suitable for further association analysis of quantitative traits in tree peony. Association analysis is a promising approach to find markers tightly linked with phenotypic traits, and the markers obtained in the present study provide foundation for molecular marker assisted breeding.