Management of a widely distributed species can be a challenge when management priorities, resource status, and assessment methods vary across jurisdictions. For example, restoration and preservation of coregonine species diversity is a goal of management agencies across the Laurentian Great Lakes. However, management goals and the amount of information available varies across management units, making the focus for management efforts challenging to determine. Genetic data provide a spatially consistent means to assess diversity. Therefore, we examined the genetic stock structure of cisco (Coregonus artedi) in the Great Lakes where the species is still extant. Using genotype data from 17 microsatellite DNA loci, we observed low levels of population structure among collections with most contributions to overall diversity occurring among lakes. Cisco from lakes Superior, Michigan, Ontario, and the St. Marys River could be considered single genetic populations while distinct genetic populations were observed among samples from northern Lake Huron. Significant within-lake diversity in Lake Huron is supported by populations found in embayments in northern Lake Huron. The Grand Traverse Bay population in Lake Michigan represents a distinct population with reduced levels of genetic variation when compared to other lakes. The different levels of within lake population structure we observed will be important to consider as future lake-specific management plans are developed.