The lignin distribution in poles of waterlogged archaeological Picea abies (L.) Karst, which was decayed by erosion bacteria (EB) under anoxic conditions for approximately 400 years, was topochemically identified by transmission electron microscopy (TEM) and high resolution UV-microspectrophotometry (UMSP). Lignin rich cell wall compartments such as cell corner (CC), compound middle lamella (CML), torus, initial pit border and mild compression wood (CW) appeared morphologically well preserved together with S1 and S3 layers and epithelial and ray parenchyma cells. Residual material (RM) from degraded S2 showed a varied lignin distribution as evidenced by the different local UV-absorbance intensities. However, evaluation of UV-absorbance line spectra of RM revealed no change in conjugation of the aromatic ring system. Presence of RM with both very low and very high lignin absorbances showed evidence for disassembly of lignin during degradation combined with aggregation of lignin fragments and physical movement of these fractions. In contrast to TEM analysis, locally decreasing lignin content was found by UMSP in CML regions.