Abstract Tree peony (Paeonia suffruticosa Andrews) is a well-known horticultural and medicinal plant. The flower buds must go through a period of endo-dormancy before bud sprouting in winter, but very little information concerned with dormancy release is available. We obtained 625,342 sequencing reads with massive parallel pyrosequencing on the Roche 454 GS FLX platform (mean length: 358.1bp). De novo assemblies yielded 23,652 contigs and singletons. 15,284 contigs longer than 300bp were further annotated, among them 12,345 ESTs showed significant similarity with sequences present in public databases (with an E-value <1e−10). 484 putative transcription factors were obtained. In addition, 2253 potential Simple Sequence Repeats (SSR) loci were identified in the 454-ESTs. Total 149 pairs of primers were designed, and 121 pairs were amplified successfully in initial screening. In addition, 73 pairs of primers displayed polymorphism. This sequence collection provides a significant resource for gene discovery during endo-dormancy of tree peony.