Poplar wood was subjected to biological treatment with a white-rot fungus Trametes hirsuta C7784. The structural features of the lignin in the untreated and treated poplar wood samples were comparatively elucidated. Milled wood lignin (MWL) and residual enzymatic lignin (REL) fractions of each sample were sequentially isolated. The total pure yields of the isolated lignin fractions after white-rot fungus treatment exceeded 96% (based on the Klason lignin content), and thus, represented the whole lignin in the fungus-treated poplar wood. The structural features of the lignin fractions were quantitatively analyzed. β–O-4′ structures were the most prominent linkage in the biologically treated wood, and there were more present than in the untreated wood. To this effect, the lignin in the fungus-treated poplar wood was easily degraded and removed under mild conditions, which is essential for subsequent conversion processes.