Intra-specific diversity of Ligularia pleurocaulis was examined from both chemical and genetic aspects, using furanoeremophilanes as the chemical index and the nucleotide sequences in the atpB-rbcL and the ITS1 regions as the genetic index. Four samples of L. pleurocaulis were collected in northwestern Yunnan, and six in southwestern Sichuan. From the ethanol extracts of the roots of all of the samples, four compounds, 6β-angeloyloxy- and 6β-tigloyloxy-furanoeremophil-1(10)-enes, and 6β-angeloyloxy- and 6β-tigloyloxy-furanoeremophil-1(10)-en-3β-ols were isolated. Further, 3β-angeloyloxyfuranoeremophil-1(10)-en-6β-ol and furanoligularenone were isolated from the Yunnan and the Sichuan samples, respectively. Two variants were found for the atpB-rbcL sequence. Base multiplicity in the ITS1 region was observed at only a few positions in the Yunnan samples, whereas it was observed at about 10 positions for the Sichuan samples. These results show that L. pleurocaulis is diverse, both chemically and genetically, and that plants in northwestern Yunnan and those in southwestern Sichuan can be distinguished by their chemical and genetic indexes.