In this paper we present results from the first in-situ Eddy Covariance measurements of air-sea CO2 exchange conducted over the 344,400 km2 Great Barrier Reef, Australia. Measurements were made in June 2009 (austral winter) and February 2010 (austral summer) using pontoon mounted eddy covariance systems at Heron Reef (23°26.577S, 151°26.577E) in the Capricorn Bunker Group of the southern Great Barrier Reef. Results show that during summer under monsoonal conditions the shallow reef flat was found to be a net source of CO2, particularly at night while the shallow and deep lagoons of Heron Reef were net sinks. Concurrent measurements of CO2 exchange over the shallow reef flat and ocean adjacent to Heron Reef found the ocean to be a CO2 sink. During winter net CO2 sequestration was found to be significantly greater than in summer. A simple CO2 budget based on these results is presented indicating that reefs such as Heron Reef in the southern Great Barrier Reef act as CO2 sinks.