These data describe the genetics of recruiting Amphiprion chrysopterus. Our goal is to score every single clownfish from the island of Moorea (we believe that the total population in Moorea is of approximately 300-500 individuals). Individuals are characterized using microsatellites, thus the data are presented as a matrix of alleles corresponding to a set of microsatellite loci. Ultimately, we want to determine the level of self-recruitment in Moorea by estimating the number of offspring which recruit on Moorea and that are derived from Moorea parents. These data are published in DOI: 10.1098/rspb.2011.2433 Beldade, R., S.J. Holbrook, R.J. Schmitt, S. Planes, D. Malone and G. Bernardi. In Press. Larger female fish contribute disproportionately more to self-replenishment. Proceedings of the Royal Society of London. Series B, Biological Sciences.