Gobiids of the genus Pomatoschistus are increasingly being investigated as models for adaptation to coastal environments and for mating system studies. Among the dozen currently analysed species, microsatellite primers have been characterized only for Pomatoschistus minutus. This paper describes seven new polymorphic loci isolated from Pomatoschistus marmoratus and Pomatoschistus microps, two species that hybridize. Cross-species amplification was tested for these new loci, together with seven already published P. minutus loci. Systematic amplification of samples of each of the three species provided a first indication of their polymorphism.