Methane (CH4) oxidation by methanotrophic bacteria in forest soils is the largest biological sink for this greenhouse gas on earth. However, the compaction of forest soils by logging traffic has previously been shown to reduce the potential rate of CH4 uptake. This change could be due to not only a decrease of methanotrophs but also an increase in methanogen activity. In this study, we investigated whether the decrease in CH4 uptake by forest soils, subjected to compaction by heavy machinery 7 years earlier, can be explained by quantitative and qualitative changes in methanogenic and methanotrophic communities. We measured the functional gene abundance and polymorphism of CH4 microbial oxidizers (pmoA) and producers (mcrA) at different depths and during different seasons. Our results revealed that the soil compaction effect on the abundance of both genes depended on season and soil depth, contrary to the effect on gene polymorphism. Bacterial pmoA abundance was significantly lower in the compacted soil than in the controls across all seasons, except in winter in the 0-10 cm depth interval and in summer in the 10-20 cm depth interval. In contrast, archaeal mcrA abundance was higher in compacted than control soil in winter and autumn in the two soil depths investigated. This study shows the usefulness of using pmoA and mcrA genes simultaneously in order to better understand the spatial and temporal variations of soil CH4 fluxes and the potential effect of physical disturbances.