Here we report the isolation of 44 microsatellites from the brooding, pocilloporid coral, Seriatopora hystrix, developed from a partial genomic DNA library using a repeat enrichment protocol. A further eight previously published microsatellites were also tested; five of these were developed for S. hystrix, whereas three were isolated from corals of the closely related genus Pocillopora. Out of these, we incorporated nine and 10 primer pairs into two multiplex reactions that reliably amplified polymorphic microsatellites in populations from the west and the east coast of Australia, respectively. Number of alleles ranged from three to 22 per locus.