Pelagic larval duration (PLD) is a commonly used proxy for dispersal potential in coral reef fishes. Here we examine the relationship between PLD, genetic structure and genetic variability in geographically widespread and ecological generalist species from one coral reef fish family (Pomacentridae) that differs in mean larval duration by more than a month. The genetic structure was estimated in eight species using a mitochondrial molecular marker (D-loop) and in a sub-set of five species using nuclear molecular markers (ISSRs). Estimates of genetic differentiation were similar among species with pelagic larvae, but differed between molecular markers. The mtDNA indicated no structure in all species except one, while the ISSR indicated some structure between the sampling locations in all species. We detected a relationship between PLD and genetic structure using both markers. These relationships, however, were caused by a single species, Acanthochromis polyacanthus, which differs from all the other species examined here in lacking a larval phase. With this species excluded, there was no relationship between PLD and genetic structure using either marker despite a range of PLDs of more than 20 days. Genetic diversities were generally high in all species and did not differ significantly among species and locations. Nucleotide diversity and total heterozygosity were negatively related to maximum PLD but again these relationships were caused by A. polyacanthus and disappeared when this species was excluded. These genetic patterns are consistent with moderate gene flow among well-connected locations and indicate that at this phylogenetic level (i.e., within family) the duration of the pelagic larval phase is unrelated to the patterns of genetic differentiation.