The relationship between thermokarst (permafrost thaw) and methane emissions from lakes and wetlands has been investigated at relatively few sites around the Arctic with highly variable results. The goal of this paper is to explore the relationship between soil carbon inputs to lakes via thermokarst erosion and methane emissions from lakes in order to explain regional-scale variability in methane emissions. Ground-based surveys of biogenic methane ebullition seeps in 75 lakes along a North-South transect in Alaska revealed that the majority of lakes emit methane via ebullition; however, geographic differences in permafrost, soil organic matter, climate and geology result in large (>10-fold) regional differences in lake methane production and emission on a lake-area basis. Thermokarst lakes that formed in icy, organic-rich Pleistocene-aged yedoma-type permafrost, common in previously unglaciated regions of Alaska, had the highest methane emissions. Non-thermokarst lakes had among the lowest levels of methane emissions. Radiocarbon ages of lake methane reflected the age of soil carbon inputs to thermokarst lakes. These results have implications for using knowledge of soil carbon storage and erosion for upscaling lake methane emissions in the Arctic.