In the ocean, large-scale dispersal and replenishment by larvae is a key process underlying biological changes associated with global warming. On tropical reefs, coral bleaching, degradation of habitat and declining adult stocks are also likely to change contemporary patterns of dispersal and gene flow and may lead to range contractions or expansions. On the Great Barrier Reef, where adjacent reefs form a highly interconnected system, we use allozyme surveys of c. 3000 coral colonies to show that populations are genetically diverse, and rates of gene flow for a suite of five species range from modest to high among reefs up to 1200 km apart. In contrast, 700 km further south on Lord Howe Island, genetic diversity is markedly lower and populations are genetically isolated. The virtual absence of long-distance dispersal of corals to geographically isolated, oceanic reefs renders them extremely vulnerable to global warming, even where local threats are minimal.