Walleye (Sander vitreus) is an important game fish in the Upper New River, with March and April walleye fishing effort from Buck Dam to Claytor Lake increasing from 49 to 66% of total fishing effort between 2007 and 2016. Population genetics research has shown the persistence of the presumptive native stock in the New River. Although the river had been stocked from sources in the Great Lakes region, unique genetic markers (microsatellite alleles at the Svi17 and Svi33 loci and mitochondrial restriction fragment haplotype 43) were observed, indicating that the native stock had persisted. Native walleye is of conservation interest due to their adaptation to a southern river system and their large ultimate size. Genetic marker-assisted selection of presumptive native walleye has been carried out since 2000, and has led to an increase in native allele frequencies from 16% and 14% in the 1997 and 1999 genetic surveys to 46% and 58% in the 2004 and 2006 surveys. Walleye abundance and angler catch increased over this time period in relation to annual stocking success. Ongoing work is aimed at deepening our understanding of population genetics and natural history of walleye in the southeast.