Samples of an intertidal zoanthid, Zoanthus coppingeri, Haddon and Shackelton, 1891, were collected from three localities in the Great Barrier Reef region during 1992–1993, and subjected to allozyme electrophoretic analysis at seven polymorphic loci. The reduced ratio of observed to expected genotypic diversity indicated that populations were partly clonal, but they were not dominated by a few clones as occurs in some other cnidarians. Regular disturbance by wave action is postulated to prevent the formation of large stands of particular clones by clearing space and mixing genotypes over small scales. The sexual origin of clonal genotypes was confirmed by conformance to Hardy-Weinberg predictions of genotype frequencies at all but one locus. Values of the standardised genetic variance among populations, FST, were highly significant between localities and between replicate sites within localities separated by only 50 m. Strong genetic structure has not previously been described in a Great Barrier Reef invertebrate species, and is considered to be the consequence of stochastic changes in gene frequencies as a result of low levels of gene flow. High clonal longevity and low recruitment rates may maintain genetic differences over long periods. Similar effects may be seen in other Great Barrier Reef invertebrate species with comparable reproductive patterns.