Breeding behaviors in birds can influence genetic diversity and so are of interest in the management of endangered species. However, egg dumping (intra-specific egg parasitism), pairing of closely related individuals, and extra-pair copulation are difficult to detect via behavioral observations, and must be corroborated with genetic information. Cooperative breeding behaviors such as helpers-at-the-nest and incubation by more than two adults, as well as other breeding behaviors such as suspected egg dumping, were recently documented in the Threatened Ae‘o (Hawaiian Stilt; Himantopus mexicanus knudseni) on the island of Moloka‘i in the Hawaiian Islands. As these behaviors are rarely observed in Charadriiformes (wading birds), in this study we compared behavioral observations of potential relationships among chicks and adults with genetic relatedness, utilizing reduced-representation sequencing and analysis of SNPs. We observed genetic evidence consistent with egg dumping, potential extra-pair copulation, and inbreeding, but were not able to assess the relatedness of extra-pair adults that contributed to incubation and nest defense. As many of the individuals in this population are color-banded and monitored regularly by local community residents, this study lays a foundation for further studies of behavior and genetic diversity in this recovering species.