Great Lakes populations of yellow perch have fluctuated throughout past decades to the present due to unstable recruitment patterns and exploitation. Our study analyzes genetic diversity and structure across the native range in order to interpret phylogeographic history and contemporary patterns. We compare complete mitochondrial DNA control region sequence) from 568 spawning individcing all 5 Great Lakes and outlying watersheds from the upper Mississippi River, Lake Winnipeg, Lake Champlain, and Atlantic and Gulf coastal relict populations. Theadces additionally are compared with fine-scale patterns from 334 individuals at 16 spawning across Lake Erie's 4 fishery management units. We identify 21 mtDNA haplotypes, including a widespread type that totals 87% of individuals across the Great Lakes. Overall genetic diversity is relatively low in comparison with other Great Lakes fishes, congruent with prior allozyme and microsatellite studies. The largest genetic demarcation separates 2 primary population groups: one in the Great Lakes, Lake Winnipeg, and upper Mississippi River watersheds and the other along the Atlantic and Gulf coasts, together with Lake Champlain; which diverged ∼ 365,000 years ago. In addition, the watersheds house genetically separable groups, whose patterns reflect broad-scale isolation by geographic distance. A few spawning groups show some fine-scale differentiation within Lake Erie, which do not reflect fishery management units and need further study with higherresolution markers.