There are many heritable phenotypic traits that are of interest for conservation, supplementation, and aquaculture of Columbia River fishes. Traits such as run timing, thermal tolerance, anadromy, and disease resistance are examples. Pedigree studies have shown strong heritability of such traits and genetic studies have identified quantitative trait loci (QTLs) and candidate loci associated with specific phenotypes. Such studies have traditionally taken years to complete in non-model species due to a lack of a reference genome and the types of genetic markers available. However, it is now possible to genotype individuals at thousands of single nucleotide polymorphisms (SNPs) in a cost effective manner using next generation sequencing technology. The RAD (Restriction site Associated DNA) sequencing approach allows for approximately 50 individual samples to be barcoded and run within the same lane of an Illumina Hi-seq instrument. Because individual samples are barcoded, the resulting sequencing data can then be analyzed to identify and genotype greater than ten thousand SNPs per sample for a given study. The data can also be used to create quality genetic maps when families of known pedigree are used. This poster describes the application of RAD sequencing for SNP identification and trait mapping in three species of Columbia River fishes; redband trout, Chinook salmon, and lamprey.