Significance Extensive release of methane from sediments of the world’s largest continental shelf, the East Siberian Arctic Ocean (ESAO), is one of the few Earth system processes that can cause a net transfer of carbon from land/ocean to the atmosphere and thus amplify global warming on the timescale of this century. An important gap in our current knowledge concerns the contributions of different subsea pools to the observed methane releases. This knowledge is a prerequisite to robust predictions on how these releases will develop in the future. Triple-isotope–based fingerprinting of the origin of the highly elevated ESAO methane levels points to a limited contribution from shallow microbial sources and instead a dominating contribution from a deep thermogenic pool.