Understanding the population structure of invasive sea lamprey (Petromyzon marinus) in the Great Lakes basin is essential for an effective control program. We review knowledge of lake connectivity, dispersal during the parasitic stage, and results from phenotypic, demographic, and genetic studies to evaluate how sea lamprey populations are structured. There is no evidence for contemporary movement between Lake Ontario and the Atlantic population, although it appears possible. Dispersal between Lake Ontario and the Finger Lakes is more likely, as is contemporary movement between Lakes Ontario and Erie via the Welland Canal, although neither has been directly observed. Downstream movement from Lake Erie to Lake Ontario via the Niagara River has been reported. Bidirectional movement between Lakes Erie and Huron has been observed, and movement of sea lamprey among the upper Great Lakes (especially between Lakes Huron and Michigan) is relatively common, although complete mixing likely does not occur. The maximum straight-line dispersal distance reported for a tagged sea lamprey was 628 km between the St. Marys River and western Lake Erie. Genetic population studies using a variety of molecular markers generally found weak but significant broad-scale population structure (e.g., between freshwater and anadromous populations, and among Lake Ontario, Lake Erie, and the upper Great Lakes), but finer-scale structure was rarely detected. Nevertheless, some within-basin structure is suggested by regional differences in phenotypic and demographic traits (e.g., sex ratio, body size). Further study will be important because management is most efficiently targeted when the geography of demographically independent populations is well-characterized.