Microbial volatile organic compounds (MVOCs) produced by the brown-rot fungus Fomitopsis palustris and white-rot fungus Trametes versicolor grown on wood chip and potato dextrose agar were analyzed by GC-MS. In total, 110 organic compounds were identified as MVOCs. Among them, only 23 were MVOCs commonly observed in both types of fungi, indicating that the fungi have differential MVOC expression profiles. In addition, F. palustris and T. versicolor produced 38 and 22 MVOCs, respectively, which were detected only after cultivation on wood chip. This suggests that the fungi specifically released these MVOCs when degrading the cell-wall structure of the wood. Time course analysis of MVOC emission showed that both types of fungi produced the majority of MVOCs during the active phase of wood degradation. As both fungi produced specific MVOCs in the course of wood degradation indicates the possibility of the application of MVOCs as detection markers for wood-decay fungus existing in woody materials.