Thermokarst lakes develop as a result of the thaw and collapse of ice-rich, permanently frozen ground (permafrost). Of particular sedimentological importance are thermokarst lakes forming in late Pleistocene icy silt (yedoma),which dramatically alter the land surface by lowering surface elevation and redistributing upland sediment into lower basins. Our study provides the first description of yedoma thermokarst lake sedimentology based on the crossbasin sampling of an existing lake. We present lake sediment facies descriptions based on data from sediment cores from two thermokarst lakes of medium depth, Claudi and Jaeger (informal names), which formed in previously non thermokarst-affected upland yedoma on the northern Seward Peninsula, Alaska. We identify four prominent facies using sedimentological, biogeochemical, and macrofossil indicators: a massive silt lacking aquatic macrofossils and other aquatic indicators situated below a sub-lacustrine unconformity (Facies 1); two basal deposits: interbedded organic silt and chaotic silt (Facies 2–3); and a silt-rich mud (Facies 4). Facies 1 is interpreted as yedoma that has thawed during lake formation. Facies 3 formed adjacent to the margin due to thaw and collapse events from the lake shore. Material from Facies 3 was reworked by wave action to form Facies 2 in a medium energy margin environment. Facies 4 formed in a lower energy environment toward the lake basin center. This facies classification and description should enhance our ability (i) to interpret the spatial and temporal development of lakes and (ii) to reconstruct long-term patterns of landscape change.