We assessed the relationship between CH4 and CO2 emission modes in 40 lakes along a latitudinal transect in Alaska to physicochemical limnology, geographic characteristics and permafrost soil types and carbon stocks surrounding lakes. We found that all lakes were net sources of atmospheric CH4 and CO2 but that the climate warming impact of lake CH4 emissions was two times higher than that of CO2. Ebullition and Diffusion were the dominant modes of CH4 and CO2 emissions respectively. Geographically, CH4 emissions from stratified, dystrophic interior Alaska thermokarst (thaw) lakes formed in icy, organic-rich yedoma permafrost soils were 6-fold higher than from non-yedoma lakes near Toolik Field Station and the rest of Alaska. Total CH4 emission was correlated with soil carbon stocks adjacent to lakes, concentrations of phosphate and total nitrogen in lake water, Secchi depth and lake area, with yedoma lakes having higher carbon stocks and nutrient concentrations, shallower Secchi depth, and smaller lake areas. Our findings suggest that permafrost type plays important roles in determining CH4 emissions from lakes by both supplying organic matter to methanogenesis directly from thawing permafrost and by enhancing nutrient availability to primary production, which can also fuel decomposition and methanogenesis.