In the ice‐rich permafrost area of Central Yakutia (Eastern Siberia, Russia), climate warming and other natural and anthropogenic disturbances have caused permafrost degradation and soil subsidence, resulting in the formation of numerous thermokarst (thaw) lakes. These lakes are hotspots of greenhouse gas emissions, but with substantial spatial and temporal heterogeneity across the Arctic. We measured dissolved CO2 and CH4 concentrations in thermokarst lakes of Central Yakutia and their seasonal patterns over a yearly cycle. Lakes formed over the Holocene (alas lakes) are compared to lakes that developed over the last decades. The results show striking differences in dissolved greenhouse gases (up to two orders of magnitude) between lake types and seasons. Shallow lakes located in hydrologically closed alas depressions acted as CO2 sinks and strong sources of diffusive CH4 during some seasons (ebullition was not assessed). Recent thermokarst lakes were moderate to extremely high sources of diffusive CO2 and CH4, with considerable accumulation of greenhouse gas under the ice cover (winter) or in the deepest water layers (summer), highlighting the need to include spring and autumn as critical periods for integrated assessments. The water column was stratified in winter (all lake types) and especially in summer (recent thermokarst lakes), generating anoxia in bottom waters and favoring CH4 production and storage, particularly in the most organic‐rich lakes. The diffusive fluxes measured from thermokarst lakes of this typical taiga alas landscape of Central Yakutia are among the highest presented across Arctic and subarctic regions