Intraspecific genetic variation among samples of six species of reef fishes,Chromis cyanea, Stegastes partitus, S. planifrons, S. leucostictus, S. dorsopunicans, andThalassoma bifasciatum collected over a 2 wk period in 1990 at La Parguera, Puerto Rico, USA and Discovery Bay, Jamaica, was evaluated using starch-gel electrophoresis. On average, products of 33 protein-coding loci were resolved in each species. Levels of polymorphism (0.95 criterion) ranged from 3.1% inS. dorsopunicans to 42.4% inC. cyanea. Estimates of genetic divergence among samples and indices of genetic subdivision were small in all six study species: mean genetic distances ranged from 0.000 to 0.002 and mean fixation indices ranged from 0.004 to 0.035. Estimates of numbers of migrants per generation (mNe) ranged from 5.1 to 11.6, indicating that substantial genetic exchange probably occurs over the relatively large geographic distance (ca. 1000 km) separating coral reef communities of La Parguera and Discovery Bay. The estimates ofmNe may be biased by a sampling strategy involving only two localities, and should therefore be interpreted with caution. With inferences based solely on allozyme frequency data under a primary assumption of neutrality, genetic substructuring of populations of the six study species on a macrogeographic scale appears virtually nonexistent.