[1] Permafrost melting is occurring in areas of the boreal forest region where large amounts of carbon (C) are stored in organic soils. We measured soil respiration, net CO₂ flux, and net CH₄ flux during May–September 2003 and March 2004 in a black spruce lowland in interior Alaska to better understand how permafrost thaw in poorly drained landscapes affects land‐atmosphere CO₂ and CH₄ exchange. Sites included peat soils underlain by permafrost at ∼0.4 m depth (permafrost plateau, PP), four thermokarst wetlands (TW) having no permafrost in the upper 2.2 m, and peat soils bordering the thermokarst wetlands having permafrost at ∼0.5 m depth (thermokarst edges, TE). Soil respiration rates were not significantly different among the sites, and 5‐cm soil temperature explained 50–91% of the seasonal variability in soil respiration within the sites. Groundcover vegetation photosynthesis (calculated as net CO₂ minus soil respiration) was significantly different among the sites (TW > TE > PP), which can be partly attributed to the difference in photosynthetically active radiation reaching the ground at each site type. Methane emission rates were 15 to 28 times greater from TW than from TE and PP. We modeled annual soil respiration and groundcover vegetation photosynthesis using soil temperature and radiation data, and CH₄ flux by linear interpolation. We estimated all sites as net C gas sources to the atmosphere (not including tree CO₂ uptake at PP and TE), although the ranges in estimates when accounting for errors were large enough that TE and TW may have been net C sinks.