The yellow perch Perca flavescens and the walleye Sander vitreus are native North American percid fishes, which have considerable fishery and ecological importance across their wide geographic ranges. Over the past century, they were stocked into new habitats, often with relative disregard for conserving local genetic adaptations. This chapter focuses on their comparative population structure and genetic diversity in relationship to historical patterns, habitat connectivity, dispersal ability, distributional abundances, and reproductive behavior. Both species possess considerable genetic structure across their native ranges, exhibiting similar patterning of discontinuities among geographic regions. The two species significantly differ in levels of genetic diversity, with walleye populations possessing overall higher genetic variability than yellow perch. Genetic divergence patterns follow the opposite trend, with more pronounced differences occurring among closely spaced spawning aggregations of yellow perch than walleye. Results reveal broad-scale correspondence to isolation by geographic distance, however, their fine-scale population structures show less relationship, often with pronounced genetic differences among some nearby reproductive groups. Genetic composition of spawning groups is stable from year to year in walleye, according to two decades of data, and is less consistent in yellow perch. These patterns appear to reflect fundamental behavioral differences between the two species.