Many species of socially monogamous birds engage in extra-pair copulations, but the extent of extra-pair paternity varies considerably by species. The ecological conditions contributing to interspecific variation in rates of extra-pair paternity remain unclear. We used a combination of single-nucleotide polymorphisms and microsatellites to document extra-pair paternity in the Banded Wren (Thryothorus pleurostictus), a socially monogamous neotropical passerine that lives in a highly seasonal environment. The rate of extra-pair paternity was relatively low, with extra-pair males siring 4% of offspring in 10% of nests. This low rate is consistent with current hypotheses predicting low rates of extra-pair paternity in nonmigratory species in which survivorship of adults is high, and it is contrary to the pattern predicted by hypotheses linking synchronous breeding with high rates of extra-pair paternity. Extra-pair males sang better and were more genetically similar to females than the males they cuckolded, though our sample size for this comparison was limited. Our data will be useful for future comparative studies examining ecological correlates of extra-pair paternity. This study also demonstrates the utility of genotyping by single-nucleotide polymorphisms as a powerful alternative to microsatellites for assessing genetic mating systems.