In comparison with windward coral reefs, the facies and evolution of leeward coral reefs has been discussed to a lesser extent. By accelerator mass spectrometry (AMS) carbon-14 dating of coral specimens collected from the trench excavated across a modern coral reef during a fishery port repair, we revealed the internal facies and Holocene evolution of a leeward reef in Ishigaki Island, Ryukyu Islands, southwest Japan. The reef facies can be split into three facies: the tabular Acropora framework facies, the tabular Acropora reworked facies, and the unconsolidated bioclast facies. The tabular Acropora reworked facies first formed a ridge by 3500 BR Then, the tabular Acropora framework facies grew both upward and seaward. The accumulation rates of the tabular Acropora framework facies ranged from 2.2 to 8.3 m/ka. Thus, the reef framework facies and accumulation rates of this leeward reef is similar to those of windward reefs, although the age of the reef top is younger than that of windward reefs.