While most population genetic studies focus on breeding populations, patterns of genetic structuring of migrating birds can provide similar insights of species distribution, yet population structuring is rarely studied at migratory stopover sites. Philopatric species such as the Eastern Phoebe (Sayornis phoebe) return to the same breeding sites, which reduces gene flow between breeding populations and leads to population structuring. Therefore, we should be able to detect population differentiation at migratory stopover sites if genetically distinct breeding populations converge during migration. Our objective was to determine if we could detect population structuring among migrating Eastern Phoebes of unknown origin. Panola Mountain State Park (PANO) is a restored grassland in central Georgia where phoebes are consistently captured throughout the annual cycle. We collected blood samples from 73 individuals at PANO between November 2017 and January 2019 and amplified 12 highly variable microsatellite loci specific to phoebes. Since the phoebes were of unknown origin captured at the same site, we assigned a priori populations based on (1) season of capture and (2) date of capture. Our FST results revealed that phoebes captured during the breeding season are genetically different compared to those captured during fall. These genetic differences are either a result of genetic differences between migratory individuals (fall and wintering seasons) and resident breeding populations (breeding season) or genetically distinct breeding populations that use PANO as a migratory site at different times. While understanding which of these is responsible for our results requires additional study, this study is the first to show population structuring of a migratory species using genetic markers at a migratory stopover site when distinct breeding grounds and populations are otherwise unknown.