Eddy covariance (EC) measurements of air-sea CO₂ exchange over desert fringing coral reefs in the Gulf of Eilat (Aqaba) (GoE), northern Red Sea, show these ecosystems are net sinks of atmospheric CO₂. This result contrasts with marine productivity models and bulk formula calculations based on water chemistry that are often used methods to determine the magnitude and direction of the CO₂ flux with the atmosphere over coral reefs. These studies have often concluded that coral reefs are net sources of CO₂ to the atmosphere with only rare cases finding otherwise. Our EC measurements find coral reefs in the GoE may absorb around 4.5 times more carbon from the atmosphere than other marine and terrestrial ecosystems and only slightly less than some tropical rainforests. This highlights the need for further direct measurements of air-sea CO₂ exchanges over coral reefs in different environmental settings so their role in the global carbon cycle can be accurately quantified.