Global warming is associated with the continued increase in the atmospheric concentrations of greenhouse gases; carbon dioxide, methane (CH4) and nitrous oxide. Wetlands constitute the largest single natural source of atmospheric CH4 in the world contributing between 100 and 231 Tg year−1 to the total budget of 503–610 Tg year−1, approximately 60 % of which is emitted from tropical wetlands. We conducted diffusive CH4 emission measurements using static chambers in river channels, floodplains and lagoons in permanent and seasonal swamps in the Okavango Delta, Botswana. Diffusive CH4 emission rates varied between 0.24 and 293 mg CH4 m−2 h−1, with a mean (±SE) emission of 23.2 ± 2.2 mg CH4 m−2 h−1 or 558 ± 53 mg CH4 m−2 day−1. These emission rates lie within the range reported for other tropical wetlands. The emission rates were significantly higher (P < 0.007) in permanent than in seasonal swamps. River channels exhibited the highest average fluxes at 31.3 ± 5.4 mg CH4 m−2 h−1 than in floodplains (20.4 ± 2.5 mg CH4 m−2 h−1) and lagoons (16.9 ± 2.6 mg CH4 m−2 h−1). Diffusive CH4 emissions in the Delta were probably regulated by temperature since emissions were highest (20–300 mg CH4 m−2 h−1) and lowest (0.2–3.0 mg m−2 h−1) during the warmer-rainy and cooler winter seasons, respectively. Surface water temperatures between December 2010 and January 2012 varied from 15.3 °C in winter to 33 °C in summer. Assuming mean inundation of 9,000 km2, the Delta’s annual diffusive emission was estimated at 1.8 ± 0.2 Tg, accounting for 2.8 ± 0.3 % of the total CH4 emission from global tropical wetlands.