Mating behavior has a profound impact on reproductive success and the resulting genetic structure of offspring. Extra-pair copulation is a widely observed behavior within avian species. This study explored the genetic effects of mating behaviors of Prothonotary warblers, Protonotaria citrea (Parulidae), using co-dominant microsatellite markers. Prothonotary warblers are migratory songbirds that build nests in cavities, commonly found in wetland habitats. A set of artificial nest boxes were initiated by Dr Robert Reilly in 2002 in Dutch Gap, Chesterfield County Virginia, USA, a tidal tributary off the James River. From this population, 28 nest boxes were surveyed yielding 47 adults and 110 offspring. All individuals were genotyped and the multilocus genotypes were used to identify parentage. Using paternity exclusion, 27.2% of offspring were identified as resulting from extra-pair mating. Surprisingly, an additional 11.8% of offspring were classified as genetically unrelated to the resident female, being presumably the result of an egg dumping from a female not caught at the nest box. The vast majority of nest boxes, 82.1% in this study, had at least one offspring that was a result of a mating behavior outside of the social pair. There was also positive spatial autocorrelation in extra-pair paternity suggesting that these matings are not randomly distributed across the sampling landscape. These data show that Protonotaria citrea engage in both extra-pair copulations and nest parasitism. Whether this is normal mating behavior for the species, or something that is unique to this population is unknown.