White and brown-rot fungi damage wood by production of enzymes that attack the structural components. The objective of this study was to characterize decay related genes and proteins that are expressed on three different wood types undergoing decay over 18 months. Variation in gene expression, presence of decay enzymes and proteins were determined for untreated pine (non-resistant), western red cedar (naturally durable), and alkaline copper quaternary (ACQ) treated pine (chemically resistant) exposed in a soil decay bed test. Decay was assessed by visual decay ratings, dynamic modulus of elasticity (MOE), and microscopy. There were no significant differences in decay between cedar and ACQ-treated pine over the 18 month period. However, there were significant differences in decay between pine and cedar and between pine and ACQtreated pine. The fungal mycelia penetrated the cell walls of pine and were continually observed over 18 months, but were not observed in cedar or ACQ-treated pine. Basidiomycetes containing decay genes lignin peroxidase (Lip), manganese peroxidase (Mnp), and laccase (Lcc) were detected on pine and ACQ-treated pine which also a greater diversity of fungi had compared to cedar. Phlebia radiata specific-lignin peroxidase and manganese peroxidase genes were expressed approximately equally on pine and ACQ-treated pine at most sampling times. The expression of P. radiata specific Lcc was higher on ACQ-treated pine than untreated pine. No basidiomycete genes were expressed and only a few basidiomycetes were identified on cedar, which also showed little decay. ACQ-treated pine also showed little decay, however basidiomycetes were present and active. Proteins were first detected on pine and ACQ-treated pine at 6 months and continued to increase through 18 months, but were not detected on cedar until 14 months exposure. There were greater numbers of total proteins on pine than on cedar and ACQ-treated pine at each time period. Decay genes were only found on pine but not on cedar and ACQ-treated pine. Additionally, the types of proteins and their score were different among the three wood types. From these results, the natural durability of cedar reduced the wood decay community and its activities. It appears that ACQ-treated wood did not stop the production of the decay enzymes but the chemical treatment did inhibit the effectiveness of the wood decay genes.