We report on the development of microsatellites in Seriatopora hystrix, a coral with algal endosymbionts. In order to obtain a genomic library free of algal DNA, we conducted a whole genome preamplification from minute amounts of symbiont-free tissue. The resulting fragments were cloned into pUC18, and Escherichia coli were transformed with the recombinant plasmids. Twenty-nine microsatellites were isolated from a library screen with a fluorescently labelled (CA)15 probe. Five of these yielded reliable polymorphic markers.