Earlier studies of the coral Pocillopora damicornis provide a conflicting picture of its use of sexual and asexual reproduction for population maintenance. In Western Australia, colonies are asexually viviparous, and populations appear to be maintained by localised asexual recruitment but founded by genotypically diverse colonists. However, on Australia¹s Great Barrier Reef (GBR), as in many other regions, populations display little or no evidence of any asexual recruitment. We used allozyme electrophoresis to test for asexual input into local populations of P. damicornis at One Tree Island on the southern GBR. Contrary to expectation we found that all of 136 planulae and 90 metamorphosed settlers from 11 reef flat and reef-crest colonies were electrophoretically identical to their broodparents. Moreover, for each colony, between 5 and 30 juveniles or settlers and their broodparent were identically heterozygous at 1 or more loci. We conclude that for the southern GBR the primary mode of reproduction involves the asexual generation of brooded larvae. However, samples of 30 adult (>15 cm) and 29 to 30 juvenile (<7 cm) colonies, from each of 4 sites, showed little evidence of asexually derived recruitment. On average, 7-locus genotypic diversity (Go:Ge; observed:expected) within samples was 90 and 81% respectively of the diversity expected for random mating, and 62% of the 238 colonies sampled displayed electrophoretically distinct phenotypes. Our data therefore challenge the established paradigm that predicts that organisms with complex life-cycles use asexual reproduction to maintain locally adapted clones and sexual reproduction to produce widely dispersed colonists.