The Great Barrier Reef (GBR) is a continental archipelagic system of 5000 reefs and shoals stretching >2000 km along the east Australia coast. The interconnectivity of these reefs should determine the choice of biological management units, which for most biota will reflect the dispersal of their eggs and/or larvae. A comparative approach using population genetics was used to ask whether the along—shore dispersal of coral reef fishes is influenced by the duration of this mobile phase. Seven species of coral reef fish, selected from three families to provide a range of taxonomic diversity and pelagic larval durations, were tested for genetic homogeneity between two regions of the GBR separated by 1000 km. A spectrum of potential dispersal capabilities was analyzed from that of Acanthochromis polyacanthus, a damselfish with brood care that uniquely lacks pelagic larvae, to that of Ctenochaetus striatus, a surgeonfish with large, specialized larvae that spend several months in the plankton. A total of 19 enzyme systems and general proteins were examined from multiple populations in each region to provide a base of 32 loci for these comparisons. With one exception, species sampled from different coral reefs within regions showed statistically significant heterogeneities across multiple loci, indicative of chaotic genetic patchiness among the samples. The exception was an anemonefish, Amphiprion melanopus, that had to be collected from large areas on each reef because of its low densities. The homogeneity of allele frequencies at local scales for this species suggests that the genetic patchiness observed in others may be a within—reef phenomenon that was manifested at the reef scale by our pseudoreplicated sampling strategy. After pooling local variability, all but two species showed significant regional differences. The exceptions were the pair (Ctenochaetus striatus, Pterocaesio chrysozona) with the longest larval durations. Acanthochromis polyacanthus showed increased variation at this larger scale, consistent with a major stock division between the two regions. The logarithm of genetic variation between northern and southern populations (measured by Weir and Cockerham's Fst was correlated with mean larval duration by an inverse linear relationship that explained 85% of the variance in the global data set. Comparison with an outgroup (Amphiprion melanopus from the Chesterfield Reefs, 1000 km east in the Coral Sea) confirmed the genetic cohesion of mainland populations for the species with shortest larval duration and shows that our empirical relationship applies only within the context of the highly connected GBR. On this basis, calculations of gene flow (Nem, the number of effective migrants per generation) between geographic regions predict panmixis for species with larval durations exceeding 1 mo. Many common species have shorter dispersal times, from which classical isolation—by—distance" models predict differentiation between northern and southern populations at genetic equilibrium. Given that modern populations...

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1. Gene flow in populations of stream insects is expected to depend on the distance between and the connectedness of sites in stream networks, and on dispersal ability (i.e. larval drift and adult flight). 2. Yoraperla brevis (Banks) is an abundant and characteristic stonefly of smaller streams in the northern Rocky Mountains. The present authors analysed genetic structure at 27 sites in sevenz streams flowing into the Bitterroot River in western Montana, USA. Cellulose acetate electrophoresis identified five variable loci with 16 alleles. 3. Genotype frequencies conformed to Hardy–Weinberg expectations. Within‐stream differentiation was low and among‐stream variation (Fst) was an order of magnitude higher. 4. UPGMA grouped sites within streams and also grouped adjacent streams. The tree produced by the Neighbour Joining Method was similar although not quite so clear cut. 5. This orderly pattern (i.e. Hardy–Weinberg proportions, homogeneity within streams and geographical structure) contrasts strongly with patterns observed in invertebrates from subtropical streams in Australia. Yoraperla brevis maintains large populations in predictable environments, has a long life‐cycle with a likelihood of cohort mixing, emerges synchronously in large breeding populations and occupies streams separated by areas of high relief; the Australian situation is the opposite in most respects. 6. Further analysis of a range of species is required to determine whether the different genetic structure in Y. brevis compared to the Australian species occurs more generally in North American stream insects.