Robust estimates of dispersal are critical for understanding whether species can migrate in response to climate change and whether gene flow will swamp natural selection and prevent local adaptation to future climate conditions. In anemonefish, recent studies have found that the parents of most offspring can be found within only a few hundred meters, suggesting that migration abilities may be much lower than previously thought for marine fish. Genetic isolation by distance patterns hold clues to dispersal abilities, but have rarely been interpreted quantitatively. In this study, we genotyped populations of a coral reef fish (Amphiprion clarkii) at 13 microsatellite loci to uncover fine-scale isolation by distance patterns in two replicate transects. We used both underwater visual censuses and observations of temporal changes in allele frequencies to estimate breeding adult population densities. Applying these effective densities with isolation by distance theory suggested that larval dispersal kernels in A. clarkii had a spread near 11 km (4-27 km) per generation. These kernels predicted low fractions of self-recruitment in continuous habitats, but the same kernels were consistent with previously reported, high self-recruitment fractions (30-60%) when realistic levels of habitat patchiness were considered. Our results suggested that ecologically relevant larval dispersal can be estimated with widely available genetic methods when effective density is measured carefully through cohort sampling and ecological censuses. Dispersal ability does not appear likely to constrain the species' ability to track climate, but local adaptation is most likely in isolated habitat patches.