Petal anthocyanins were systematically identified and characterized by high-performance liquid chromatography (HPLC)–electrospray ionization–mass spectrometry (MS) coupled with diode array detection among nine wild herbaceous peony (Paeonia L.) species (15 accessions). Individual anthocyanins were identified according to the HPLC retention time, elution order, MS fragmentation patterns, and by comparison with authentic standards and published data. Six main anthocyanins, including peonidin-3,5-di-O-glucoside, peonidin-3-O-glucoside-5-O-arabinoside (Pn3G5Ara), peonidin-3-O-glucoside, pelargonidin-3,5-di-O-glucoside, cyanidin-3,5-di-O-glucoside, and cyanidin-3-O-glucoside (Cy3G), were detected. In addition to the well-known major anthocyanins, some minor anthocyanins were identified in herbaceous peony species for the first time. Detection of the unique anthocyanins cyanidin-3-O-glucoside-5-O-galactoside and pelargonidin-3-O-glucoside-5-O-galactoside in both Paeonia anomala L. and P. anomala ssp. veitchii (Lynch) D.Y. Hong & K.Y. Pan indicated these two species should belong to the same taxon. Pn3G5Ara was found only in European wild species and subspecies suggesting different metabolic pathways between European and Chinese accessions. Anthocyanins conjugated with galactose and arabinose were observed in the genus Paeonia for the first time. The North American species, Paeonia tenuifolia L., had high Cy3G content in flower petals. This anthocyanin composition is distinct from the anthocyanin composition in Asian and European species and possibly is responsible for the vivid red coloration in flowers.