There is growing evidence that hybridization not only by means of allopolyploidy but also at the homoploidy level was a major driving force of plant diversification. While allopolyploidy is known to be a common mode of speciation in Paeonia (Paeoniaceae), hybrid speciation at the diploid level needs further evaluation. Paeonia anomala was previously considered to be an interspecific hybrid but with an unknown ploidy level. In this study P. anomala is identified as a diploid (2n = 10). With increased sampling of populations and molecular markers, we showed that P. anomala is a homoploid hybrid that originated from a cross between P. veitchii and P. lactiflora. Five populations of P. anomala were sequenced for the following molecular markers: the matK gene and two intergenic spacers, psbA-trnH and rps16-trnQ, of the chloroplast genome; the internal transcribed spacers (ITS) of nuclear ribosomal DNA; and three low-copy nuclear genes, Adh1, Adh2, and Gpat. The populations of P. anomala were grouped together with P. veitchii on the ITS and Gpat phylogenies but with P. lactiflora on the chloroplast phylogeny. Sequence polymorphism was found at the Adh1 and Adh2 loci within individuals of P. anomala. These polymorphic sequences were grouped with P. veitchii and P. lactiflora, respectively. Phenetic analysis indicated that P. anomala is morphologically similar to P. veitchii. Phenotypic evolution resulting from the combination of two diverged genomes might have occurred primarily at the physiological level and allowed P. anomala to adapt to geographic regions different from those of its parents.