Arctic permafrost-associated wetlands and thawing permafrost emit the greenhouse gas methane (CH4), either as a product of recent microbial activity in the active layer or taliks, or from deeper geogenic sources where pathways through the permafrost exist. Current emission estimates vary strongly between different models and there is still disagreement between bottom-up estimates from local field studies and top-down estimates from atmospheric measurements. We use airborne flux data from two campaigns in the Mackenzie River Delta, Canada, in July 2012 and 2013 to directly quantify permafrost CH4 emissions on the regional scale, to analyse the regional pattern of CH4 fluxes and to estimate the contribution of geogenic emissions to the overall CH4 budget of the delta. CH4 fluxes were calculated with a time-frequency resolved version of the eddy covariance technique, resulting in a gridded 100 m x 100 m resolution flux map within the footprints of the flight tracks. We distinguish geogenic gas seeps from biogenic sources by their strength and show that they contribute strongly to the annual CH4 budget of the delta. Our study provides the first estimate of annual CH4 release from the Mackenzie River Delta and the adjacent coastal plain. We show that one percent of the covered area contains the strongest geogenic seeps which contribute disproportionately to the annual emission estimate. Our results show that geogenic CH4 emissions might need more attention, especially in areas where permafrost is vulnerable to thawing sufficiently to create pathways for geogenic gas migration. The presented map can be used as a baseline for future CH4 flux studies in the Mackenzie River Delta.