Mangrove forests are highly productive tropical and subtropical coastal systems that provide a variety of ecosystem services, including the sequestration of carbon. While mangroves are reported to be the most intense carbon sinks among all forests, they can also support large emissions of greenhouse gases (GHGs), such as carbon dioxide (CO2) and methane (CH4), to the atmosphere. However, data derived from arid mangrove systems like the Red Sea are lacking. Here, we report net emission rates of CO2 and CH4 from mangroves along the eastern coast of the Red Sea and assess the relative role of these two gases in supporting total GHG emissions to the atmosphere. Diel CO2 and CH4 emission rates ranged from −3452 to 7500 µmol CO2 m−2 d−1 and from 0.9 to 13.3 µmol CH4 m−2 d−1 respectively. The rates reported here fall within previously reported ranges for both CO2 and CH4, but maximum CO2 and CH4 flux rates in the Red Sea are 10- to 100-fold below those previously reported for mangroves elsewhere. Based on the isotopic composition of the CO2 and CH4 produced, we identified potential origins of the organic matter that support GHG emissions. In all but one mangrove stand, GHG emissions appear to be supported by organic matter from mixed sources, potentially reducing CO2 fluxes and instead enhancing CH4 production, a finding that highlights the importance of determining the origin of organic matter in GHG emissions. Methane was the main source of CO2 equivalents despite the comparatively low emission rates in most of the sampled mangroves and therefore deserves careful monitoring in this region. By further resolving GHG fluxes in arid mangroves, we will better ascertain the role of these forests in global carbon budgets.