Walleye (Sander vitreus) is a heavily managed fishery, the genetic integrity of which has been affected by introductions of nonnative stocks via hatchery supplementation. DNA analysis on walleye has revealed highly divergent populations of walleye in the Ohio and New rivers. The focus of this project is to identify the distribution and assess the introgression of native walleye populations in West Virginia. PCR-RFLP analysis of mtDNA reveals native walleye are distributed throughout West Virginia, with higher frequencies in the Kanawha/New River system. Analysis of microsatellite DNA markers suggests native walleye stocks within the Ohio and Monongahela Rivers have introgressed with introduced walleye populations. Native walleye stocks in the Kanawha and New Rivers are relatively uninfluenced. The stocks in the Kanawha/New River system should be used for future hatchery supplementation and restoration of a native population of walleye in West Virginia.