Petal pigment compositions were used as markers to study the phenetic relationships among seven wild tree peony species of Paeonia section Moutan DC. (fifteen accessions) from China. As the pigment markers, five anthocyanins together with three flavone and three flavonol aglycones were used. Principal component analysis (PCA) provided five eigenvectors from nineteen pigment patterns, in which peonidin and cyanidin as well as the types of glycosides greatly influenced the first factor, Z1. The Euclidean distances of standardized values obtained by eigenvector matrices with five factors (Zl to Z5) produced a dendrogram in Ward's minimum variance cluster analysis, which showed good agreement with a classification based on the morphological characteristics of two subsections Vaginatae F.C. Stern and Delavayanae F.C. Stern. The results obtained by PCA and clustering qualify a chemical classification of section Moutan using secondary metabolites, specifically flower pigments, as taxonomic markers.