Eleven family groups (n = 22 adults, 28 chicks) of North American Black Terns (Chlidonias niger surinamensis) were genotyped at four polymorphic loci in a pilot study to determine the genetic mating system of this socially monogamous species. Samples were collected between 2003 and 2008 at two colony sites in Wisconsin (USA) that differed in structural complexity of the breeding habitat and nest density, and from families in which the adult males (putative fathers) varied with respect to body condition. Thus, both ecological and individual variations were explored as possible factors influencing the extent of extra-pair paternity. No mismatched alleles were detected, however, between chicks and their putative parents, suggesting that extra-pair paternity is negligible in this subspecies. Despite the small sample size, the combined probability of detecting an allelic exclusion at one or more loci was 0.998, indicating sufficient power to detect a case of extra-pair paternity if it occurred. Data obtained from recaptures of adults banded over a 10-year period (2000–2009) indicated that inter-year mate retention was low (∼20%) and was observed only in pairs that remained together in consecutive years. No “divorced” mates of recaptured adults were encountered in subsequent years, suggesting that frequent mate switching is due more to the death or disappearance of the mate than to intentional dissolution of the pair bond. The results of this pilot study provide the first evidence of genetic monogamy in Black Terns and suggest that low mate fidelity is related to low breeding site fidelity, a characteristic common in birds that breed in unstable habitats.