Six Ligularia fischeri samples, two from Sichuan (samples 1 and 2) and four from Chongqing (samples 3-6), were examined for root chemicals and the DNA sequence of the internal transcribed spacers of the ribosomal RNA gene. Samples 2 and 3 contained benzofurans. The isolation of benzofurans shows that the chemical diversity in L. fischeri is higher than previously reported. Samples 1, 4, 5, and 6 contained eremophilanes. However, the compounds were different between sample 1 and samples 4-6, indicating variation within eremophilane producers. DNA data indicated that introgression could be a mechanism of benzofuran production in sample 2 and that sample 1 and samples 4-6 were genetically separate.