Samples of Castanea, Fraxinus and Torreya wood from excavations in central Japan that had been buried by sediments in a waterlogged condition for 5,500 to 12,000 years were found to be decayed by different forms of wood-destroying bacteria. Tunnels in the secondary wall of Fraxinus and samples of Castanea and Torreya was a type of decay where bacteria penetrated the S3 layer and moved into the secondary wall. Minute cavities were formed in the S1 and S2 layers and a diffuse degradation of the entire secondary wall, causing a preferential degradation of polysaccharides, was evident. In some cells, the residual lignin matrix of the secondary wall maintained aspects of its original orientation allowing the S1 and S2 to be easily differentiated, however, in others the secondary wall was extensively eroded. The S3 layer persisted in the degraded cells from the heartwood of Castanea and Fraxinus samples. The middle lamella remained relatively intact but frequently appeared thin, less electron dense and did not retain its original rigid structure. Degradation observed in Torreya was less severe than in other woods. The secondary wall was eroded and individual secondary wall layers were not discernible. Decay patterns in all the ancient buried woods had characteristics of decay caused by erosion bacteria, and these organisms appear to be the primary agents responsible for the degradation observed.