It has long been hypothesized that Western Australian coral reefs are genetically connected to those in Indonesia via long-distance dispersal, and that this connection may influence the timing of annual mass coral spawning on Western Australian coral reefs. This genetic connection has not been tested, and it requires re-evaluation because spawning patterns of Western Australian corals are not as synchronous or seasonal as originally thought. Here, we used population genetics to examine patterns of gene flow among populations of the scleractinian coral Acropora tenuis in Indonesia and Western Australia. Analysis of microsatellite data showed that Indonesian and Australian populations are highly genetically differentiated. Importantly, this genetic divergence is associated with differences in the seasonal spawning time of A. tenuis between the two regions, with Indonesian populations dominated by ‘spring’ spawners and Western Australian populations dominated by ‘autumn’ spawners, indicating that spawning season has an important influence on genetic structure. Furthermore, negligible gene flow between Indonesia and Western Australia indicates that the recolonization of inshore Western Australian populations since the Last Glacial Maximum was independent of input from Indonesian populations.