Coastal marine reserves in general, and coral reef reserves in particular, are typically composed of scattered patches separated by uninhabited areas. Due to the sessile mode of life of adult corals, larval connectivity is often the only agent of gene flow between reef localities. In this study we examined the connectivity between populations of the common scleratinian coral Stylophora pistillata at the northern tip of the Gulf of Aqaba (Red Sea), using the rDNA ITS (internal transcribed spacer) as a molecular marker. Sequence comparisons among recruits indicated very similar, equally-diverse, assemblages of recruits in both the northern (highly affected by anthropogenic disturbances) and southern (less affected) study sites, implying a high larval connectivity or common sources of larval supply. By contrast, sequence diversity observed among adults declined sharply from southern to northern sites, accompanied by genetic differentiation of the respective populations. Based on Fu's Fs-test of selective neutrality, it may be suggested that various post-settlement selective regimes, presumably more intense in the northern sites, provide a reasonable explanation for the observed patterns of genetic diversity. The suggested hypothesis is supported by the sharper decline in sequence diversity found between recruits and adults in the northern sites. This study exemplifies the necessity to consider local selective factors, in addition to larval connectivity, when managing marine reserves.