Hylomecon japonica (Papaveraceae) is the sole species of its genus. Two varieties, H. japonica var. dissecta and H. japonica var. subincisa, have been recognized, but the presence of numerous morphological intermediates renders the intraspecific taxa controversial. Based on observations of natural populations and molecular sequences of nDNA (NADPH) and cpDNA (rpoB-trnC and trnG intron regions), our results show that the samples identified as distinct varieties are scattered and nested within the subclades of plants identified as H. japonica var. japonica. As a whole, all samples of H. japonica are monophyletic; this is further supported by the continuous variation in leaf morphology. As a result, the two infraspecific names are synonymized with H. japonica. Our study emphasizes the importance of evaluating the full range of morphological variation and molecular data when describing infraspecific taxa within a morphologically variable species.