Accurate measures of relatedness and inbreeding are important when managing the genetic health of endangered species. However undetected extra-pair parentage, where offspring are the result of copulations outside of the social pair, may result in inaccuracies in relatedness measures if these data are obtained through observing social pairings. Genetic markers present a useful method to detect extra-pair parentage and confirm the accuracy of observed social family groups. With the development of species-specific polymorphic microsatellite loci for the socially monogamous Chatham Island Black Robin (Petroica traversi), it is now possible to investigate extra-pair parentage in this species. Microsatellite genotyping of social family groups allowed us to identify extra-pair paternity in the population on Rangatira Island. The occurrence of extra-pair paternity may have implications for conservation management of this endangered species, as the number of adults contributing to the gene pool is likely different than would be expected from available social pedigree data. While a pedigree is often the best available source of relatedness information for endangered species, it is recommended that where possible, genetic tools should be used to verify pedigree data when informing conservation management decisions.