A new sesquiterpenoid substituted with unsaturated ester, guaiaglehnin A (1), along with 15 previously known compounds, were isolated from the methanol extract of the terrestrial part of Eupatorium glehnii (Compositae) collected in Nagano Prefecture, Japan, the results of which supported the previous study by Takahashi et al. The chemical constituents of E. glehnii collected in Nagano Prefecture and those collected in Tokushima or Hokkaido are quite different, depending on collection site, although the species are identical. The base sequences of three different samples were identical. Diversity in the chemical components was detected, though no diversity existed in the DNA sequence. In this study, eupasimplicin A (2) was also isolated, whose presence in the extract of E. chinense simplicifolium was recorded but not in an article. The side chain geometry of hiyodorilactone B (5) was revised to be E.