Abstract Four seeps and mud extrusion features at the lake floor were discovered in August 1999 in the gas hydrate area in Lake Baikal's South Basin. This paper describes these features in detail using side-scan sonar, detailed bathymetry, measurements of near-bottom water properties, selected seismic profiles and heat flow data calculated from the depth of the hydrate layer as well as obtained from in situ thermoprobe measurements. The interpretation of these data is integrated with published geochemical data from shallow cores. The seeps are identified as methane seeps and appear as mud cones (maximum 24 m high, 800 m in diameter) or low-relief craters (maximum 8 m deep, 500 m in diameter) at the lake floor. Mud cones (estimated to be approximately 50–100 ka old) appear to be older than the craters and have a different structural setting. Mud cones occur at the crest of rollover structures, in the footwall of a secondary normal fault, while the craters occur at fault splays. The seeps are found in an area of high heat flow where the base of the gas hydrate layer shallows rapidly towards the vent sites from about 400 m to about 160 m below the lake floor. At the site of the seep, a vertical seismic chimney disrupts the sedimentary stratification from the base of the hydrate layer to the lake floor. Integration of these results leads to the interpretation that focused destabilization of gas hydrate caused massive methane release and forced mud extrusion at the lake floor and that the gas seeps and mud diapirs in Lake Baikal do not have a deep origin. This is the first time that methane seeps and/or mud volcanoes associated with gas hydrate decomposition have been observed in a sub-lacustrine setting. The finding suggests that gas hydrate destabilization can create large pore fluid overpressures in the shallow subsurface (<500 m subsurface) and cause mud extrusion at the sediment surface.