The relationship between biogeochemical process rates and microbial functional activity was investigated by analysis of the transcriptional dynamics of the key functional genes for methanogenesis (methyl coenzyme M reductase; mcrA) and methane oxidation (particulate methane monooxygenase; pmoA) and in situ methane flux at two peat soil field sites with contrasting net methane-emitting and -oxidizing characteristics. qPCR was used to quantify the abundances of mcrA and pmoA genes and transcripts at two soil depths. Total methanogen and methanotroph transcriptional dynamics, calculated from mcrA and pmoA gene : transcript abundance ratios, were similar at both sites and depths. However, a linear relationship was demonstrated between surface mcrA and pmoA transcript dynamics and surface flux rates at the methane-emitting and methane-oxidizing sites, respectively. Results indicate that methanotroph activity was at least partially substrate-limited at the methane-emitting site and by other factors at the methane-oxidizing site. Soil depth also contributed to the control of surface methane fluxes, but to a lesser extent. Small differences in the soil water content may have contributed to differences in methanogen and methanotroph activities. This study therefore provides a first insight into the regulation of in situ, field-level surface CH(4) flux at the molecular level by an accurate reflection of gene : transcript abundance ratios for the key genes in methane generation and consumption.