During the last glacial cycle, greenhouse gas concentrations fluctuated on decadal and longer timescales. Concentrations of methane, as measured in polar ice cores, show a close connection with Northern Hemisphere temperature variability, but the contribution of the various methane sources and sinks to changes in concentration is still a matter of debate. Here we assess changes in methane cycling over the past 160,000 years by measurements of the carbon isotopic composition δ13C of methane in Antarctic ice cores from Dronning Maud Land and Vostok. We find that variations in the δ13C of methane are not generally correlated with changes in atmospheric methane concentration, but instead more closely correlated to atmospheric CO2 concentrations. We interpret this to reflect a climatic and CO2-related control on the isotopic signature of methane source material, such as ecosystem shifts in the seasonally inundated tropical wetlands that produce methane. In contrast, relatively stable δ13C values occurred during intervals of large changes in the atmospheric loading of methane. We suggest that most methane sources—most notably tropical wetlands—must have responded simultaneously to climate changes across these periods.