Soils in Southeast Alaska contain some of the world’s highest concentrations of organic matter; however, the balance between carbon-sequestering net primary production and greenhouse gas (GHG)-emitting soil respiration in this region may shift due to climate change. We conducted a metagenomic survey of microbial respiratory marker gene abundances in soils from several ecosystem types in the carbon (C)-rich perhumid coastal temperate rainforest (PCTR) of Southeast Alaska in order to better understand microbial controls on GHG emissions in the context of a vulnerable soil C stock. Landscape-scale variability in aerobic respiration, methanogenesis, and denitrification marker genes across ecosystem types was most significantly related to gradients in soil moisture and pH. We found that the aerobic respiration marker gene A1-type heme-copper oxidase was associated with measured summertime carbon dioxide (CO2) emissions and the methanogenesis marker gene mcrA was associated with summertime methane (CH4) emissions. Denitrification marker genes nirK, nirS, cNor, qNor, and nosZ were not associated with measured nitrous oxide (N2O) emissions; however, denitrification marker gene abundance was associated with denitrification activity as measured by denitrification enzyme assays. Denitrification activity was shown to be strongly controlled by nitrate rather than denitrifying community composition. This study demonstrates the utility of microbial respiratory marker genes in understanding where in the landscape the greatest emissions of the greenhouse gases CO2, CH4, and N2O likely occur and what soil properties regulate microbially-mediated GHG emissions.