Many recent studies have employed molecular markers to uncover important aspects of mating systems in teleost fishes. The fathead minnow (Pimephales promelas) is a nest-building North American cyprinid that spawns multiply and exhibits exclusive male parental care. A battery of microsatellite markers was developed to analyse paternity in this species. The seven characterized loci possess four to 31 alleles and expected heterozygosities of 0.455-0.974. In combination, they elicit an exclusion probability of 0.999, a desirable level for paternity analysis. In addition, cross-amplifications were conducted to test primer efficacy in 13 other taxa, including two congeners.