Population genetic structure can aide in developing conservation and management strategies by characterizing populations on local and regional scales. The Elegant Tern (Thalasseus elegans) has a restricted breeding range, with a majority of its nesting population historically found on Isla Rasa, Gulf of California, Mexico. Since the late 1950s, increased frequency of low marine productivity due to warm oceanographic anomalies, such as El Niño events, have caused northward expansion of Elegant Tern breeding colonies into southern California, USA. To test the hypothesis that high gene flow occurs between Gulf of California and southern California Elegant Tern breeding colonies, restriction-site associated DNA sequencing was used to analyze 5,510 single nucleotide polymorphisms from 69 Elegant Terns sampled across four known breeding sites: