The EPIC strategy was used in the present study in order to develop molecular markers for Epinephelus itajara. Twelve primers were designed for six genomic regions. The results of the study provide a number of appropriate new nuclear DNA markers for future genetic studies in several endangered/overexploited grouper species. The description of these markers will also expand the number of molecular tools available for the reconstruction of the life history of the different grouper species, in particular those in urgent need of effective protection measures.