The increase of atmospheric methane (CH4) and carbon dioxide (CO2), two of the main anthropogenic greenhouse gases, is largely driven by fossil sources. Sources and sinks remain insufficiently characterized in the Mediterranean and Middle East areas, where very few in situ measurements are available. We measured the atmospheric mixing ratios of CH4 and CO2 by ship in the region in July and August 2017. High mixing ratios were observed over the Suez Canal, Red Sea and Arabian Gulf, while generally lower mixing ratios were observed over the Gulf of Aden and Gulf of Oman. We probe the origin of the CO2 and CH4 excess mixing ratio by using correlations with light alkanes and through the use of a Lagrangian model coupled to two different emission inventories of anthropogenic sources. We find that the CO2 and especially the CH4 enhancements are mainly linked to nearby oil and gas (OG) activities over the Arabian Gulf and a mixture of other sources over the Red Sea. The isomeric ratio of pentane is shown to be a useful indicator of the OG component of atmospheric CH4 at the regional level. Upstream emissions linked to oil in the northern Arabian Gulf seem to be underestimated, while gas-related emissions in the southern Gulf are overestimated in our simulations. Our results highlight the need for improvement of inventories in the area to better characterize the changes in magnitude and the complex distribution of the OG sources in the Middle East.