Technical Abstract: The use of molecular genetic technologies for broodstock management and selective breeding of aquaculture species is becoming increasingly more common with the continued development of genome tools and reagents. Several laboratories have produced genetic maps for rainbow trout to aid in the identification of loci affecting phenotypes of interest. These maps have resulted in the identification of many quantitative/qualitative trait loci affecting phenotypic variation in traits associated with albinism, disease resistance, temperature tolerance, sex determination, embryonic development rate, spawning date, condition factor and growth. Unfortunately, the elucidation of the precise allelic variation and/or genes underlying phenotypic diversity has yet to be achieved in this species having low marker densities and lacking a whole genome reference sequence. Experimental designs which integrate segregation analyses with linkage disequilibrium (LD) approaches facilitate the discovery of genes affecting important traits. To this end, the extent of LD has been characterized for humans and several agriculturally important livestock species including cattle, sheep, chickens, and pigs. All of these results indicate that large numbers of markers from high-density maps are required to identify genes of interest using whole genome association studies in these species. Characterizing the extent of LD in the NCCCWA rainbow trout broodstock population will enable the use of integrated mapping approaches and facilitate the identification of genes affecting traits of interest by determining the required marker density to perform genome wide association scans.