The Wood Stork Mycteria americana is a rare resident bird species in the Caribbean, where it has small population sizes and reduced genetic variability. In the present study, we inferred the mating systems of the only two breeding colonies of Wood Stork known in the Caribbean, which are located in two of its most important wetlands: the Zapata Swamp Wetland and the Sabana-Camagüey Archipelago, both in Cuba. We sampled growing feathers of 27 chicks from 11 nests and analyzed genetic data from the most variable autosomal microsatellite loci described for the species. We estimated the relatedness between chicks by using the Queller-Goodnight coefficient and two maximum likelihood methods of kinship reconstruction. Evidence of monogamy was found in 27% of the nests analyzed, nest parasitism in the 36%, and extra-pair paternity in the 18%, while for the rest, inconsistencies among the methods were detected. Our results constitute the first evidence of extra-pair paternity for the Wood Stork and corroborate the usefulness of a non-invasive approach to perform kinship analysis in a poorly studied species.