Genetic diversity is a critical cornerstone of biodiversity and is a central goal in management and conservation biology. Such diversity has implications for survivability, adaptability, and resiliency of a species. This study aimed to determine levels of genetic diversity and population genetic structure in the Northern Black Swift (Cypseloides niger borealis). This species nests across western North America as far north as Canada and south into Mexico, migrating annually to wintering areas in western Brazil. Colonies occur in isolated areas where appropriate nesting habitat is available, and in many cases, colonies are widely separated from each other. Banding data revealed that adults of this long-lived species return to their same breeding colony annually for many years. Additionally, some females exhibit natal philopatry, returning to and successfully raising offspring at the colony where they were hatched. This allowed us to hypothesize that we might expect some amount of genetic structure in the samples we studied. The life history characteristics of this species suggest that breeding colonies might be more genetically differentiated than other migratory birds that tend to have limited population genetic structure across their ranges. We used newly developed species-specific microsatellite primers to examine levels of genetic diversity and connectivity among 6 Black Swift colonies in the western United States. Levels of genetic diversity were generally high (expected heterozygosity ranging from 0.67 to 0.75) and comparable across 3 breeding sites with sufficient sample sizes (N > 5). Principal coordinates analysis and STRUCTURE analysis showed no real clustering of individuals in regard to colonies, suggesting one panmictic metapopulation rather than multiple populations that are genetically distinct as we had previously hypothesized based on banding data. This is the first study to elucidate the genetic structure among colonies of Black Swift.