Background: Conserving genetic diversity and local adaptations are management priorities for wild populations of exploited species, which increasingly are subject to climate change, habitat loss, and pollution. These constitute growing concerns for the walleye Sander vitreus, an ecologically and economically valuable North American temperate fish with large Laurentian Great Lakes' fisheries. This study compares genetic diversity and divergence patterns across its widespread native range using mitochondrial (mt) DNA control region sequences and nine nuclear DNA microsatellite (μsat) loci, examining historic and contemporary influences. We analyze the genetic and morphological characters of a putative endemic variant– “blue pike” S. v. “glaucus” –described from Lakes Erie and Ontario, which became extinct. Walleye with turquoise-colored mucus are evaluated, since some have questioned whether these are related to the “blue pike”. Results: Walleye populations are distinguished by significant considerable genetic divergence (mean FST mtDNA=0.32±0.01, μsat=0.13±0.00) and substantial diversity across their range (mean heterozygosity mtDNA=0.53±0.02, μsat=0.68±0.03). Southern populations markedly differ, possessing unique haplotypes and alleles, especially the . The Ohio/New River population that housespossesses the most pronounced divergence and the oldest haplotype. Northerly formerly glaciated populations have greatest diversity in Lake Erie (mean heterozygosity mtDNA=0.79±0.00, μsat=0.72±0.01). Genetic diversity was much less in historic Lake Erie samples from 1923–1949 (mean heterozygosity mtDNA=0.05±0.01, μsat=0.47±0.06) than today. The historic “blue pike” had no unique haplotypes/alleles and there is no evidence that it comprised a separate taxon from walleye. Turquoise mucus walleye also show no genetic differentiation from other sympatric walleye and no correspondence to the “blue pike”. Conclusions: Contemporary walleye populations possess high levels of genetic diversity and divergence, despite habitat degradation and exploitation. Genetic and previously published tagging data indicate that natal homing and spawning site philopatry led to population structure. Population patterns were shaped by climate change and drainage connections, with northern ones tracing to post-glacial recolonization. Southerly populations possess unique alleles and may provide an important future genetic reservoir. Allelic frequencies of Lake Erie walleye from ~70–90 years ago significantly differed from today, suggesting population recovery after extensive habitat loss, pollution, and exploitation. The historic “blue pike” was indistinguishable from walleye, indicating that taxonomic designation is not warranted.