The transition from the last glacial and beginning of Bølling–Allerød and Pre-Boreal periods in particular is marked by rapid increases in atmospheric methane (CH4) concentrations. The CH4 concentrations reached during these intervals, ∼650–750 ppb, is twice that at the last glacial maximum and is not exceeded until the onset of industrialization at the end of the Holocene. Periods of rapid sea-level rise as the Last Glacial Maximum ice sheets retreated and associated with ‘melt-water pulses’ appear to coincide with the onset of elevated concentrations of CH4, suggestive of a potential causative link. Here we identify and outline a mechanism involving the flooding of the continental shelves that were exposed and vegetated during the glacial sea-level low stand and that can help account for some of these observations. Specifically, we hypothesize that waterlogging (and later, flooding) of large tracts of forest and savanna in the Tropics and Subtropics during the deglacial transition and early Holocene would have resulted in rapid anaerobic decomposition of standing biomass and emission of methane to the atmosphere. This novel mechanism, akin to the consequences of filling new hydroelectric reservoirs, provides a mechanistic explanation for the apparent synchronicity between rate of sea-level rise and occurrence of elevated concentrations of ice core CH4. However, shelf flooding and the creation of transient wetlands are unlikely to explain more than ∼60 ppb of the increase in atmospheric CH4 during the deglacial transition, requiring additional mechanisms to explain the bulk of the glacial to interglacial increase. Similarly, this mechanism has the potential also to play some role in the rapid changes in atmospheric methane associated with the Dansgaard–Oeschger cycles. Copyright © 2012 John Wiley & Sons, Ltd.