Most studies of greenhouse gas fluxes from forest soils in the coastal rainforest have considered carbon dioxide (CO2), whereas methane (CH4) has not received the same attention. Soil hydrology is a key driver of CH4 dynamics in ecosystems, but the impact on the function and distribution of the underlying microbial communities involved in CH4 cycling and the resultant net CH4 exchange is not well understood at this scale. We studied the growing season variations of in situ CH4 fluxes, microbial gene abundances of methanotrophs (CH4 oxidizers) and methanogens (CH4 producers), soil hydrology, and nutrient availability in three typical forest types across a soil moisture gradient. CH4 displayed a spatial variability changing from a net uptake in the upland soils (3.9–46 µmol CH4 m−2 h−1) to a net emission in the wetter soils (0–90 μmol CH4 m−2 h−1). Seasonal variations of CH4 fluxes were related to soil hydrology in both upland and wet soils. Thus, in the upland soils, uptake rates increased with the decreasing soil moisture, whereas CH4 emission was inversely related to the water table depth in the wet soils. Spatial variability of CH4 exchange was related to the abundance of genes involved in CH4 oxidation and production, but there was no indication of a temporal link between microbial groups and CH4 exchange. Our data show that the abundances of genes involved in CH4 oxidation and production are strongly influenced by soil moisture and each other and grouped by the upland–wetland classification but not forest type