We present methane mixing ratio and δ13C time series measured at Baring Head, New Zealand, and Scott Base, Antarctica, over the years 1991–2003. These data demonstrate that the apparent kinetic isotope effect (KIE) of the methane atmospheric sink (derived from the amplitudes of the mixing ratio and δ13C seasonal cycles) is generally much larger than would be expected if the sink were the hydroxyl radical alone and has changed significantly during the observation period on a timescale of ∼3 years. We show using a global transport model that this technique for deriving the KIE should be quite accurate for a single atmospheric sink and that the change with time is unlikely to arise from El Niño–Southern Oscillation transport effects. We infer that a sink in addition to hydroxyl is required. A strong candidate for this extra sink is atomic chlorine in the marine boundary layer (MBL). We derive the amplitude of the chlorine concentration seasonal cycle that would fully account for the apparent KIE. This amplitude ranges from ∼104 atom cm−3 in 1994–1996 to about 3 × 103 atom cm−3 in 1998–2000. If the KIE is enhanced throughout the free troposphere, the seasonal mean concentrations of atomic chlorine required in the MBL would be about 3 × 104 atom cm−3 in 1994–1996 and ∼104 atom cm−3 in 1998–2000.