We report the development of 10 polymorphic molecular markers containing short tandem repeats in the cosmopolitan reef-building coral, Pocillopora damicornis, an important model species for coral health, physiology, ecology, and genetics. The availability of polymorphic DNA markers in P. damicornis can act as impetus for investigations into inheritance and population genetics, as well as novel investigations into host-symbiont ecology and evolution. Coral bleaching and gene flow studies performed with these markers can have direct conservation implications. © 2007 The Authors.