Thermokarst lakes are widespread features of changing periglacial environments. In this study, we analyze total organic carbon content (TOC), C/N, stable carbon isotopes and methane concentration in pore water from sediments of 18 tundra lakes in West Alaska and 11 boreal lakes in Central Alaska in order to discuss differences in carbon accumulation, sources of organic matter and their role in the carbon cycle. While a wide range of TOC content was measured in West Alaska with highest TOC in lakes that initiated in drained lake basins, some boreal lakes in Central Alaska, like Goldstream Lake show surprisingly low TOC. Similar finding in CH4 concentration suggest that state of permafrost, the age of the lakes and the catchment characteristics have an important influence on sources of organic carbon and, thus, different potential of thermokarst lakes to contribute to the global carbon cycle.