Coral reefs are considered to be a source of atmospheric carbon dioxide because of their high calcium carbonate production and low net primary production. This was tested by direct measurement of diurnal changes in the partial pressure of carbon dioxide (P-CO2) in reef waters during two 3-day periods; one in March 1993 and one in March 1994, on Shiraho reef of the Ryukyu Islands, Japan. Although the P-CO2 values in reef waters exhibited large diurnal changes ranging from 160 to 520 microatmospheres, they indicate that the reef flat area is a net sink for atmospheric carbon dioxide. This suggests that the net organic production rate of the reef community exceeded its calcium carbonate production rate during the observation periods.