Bacterial cold water disease (BCWD) causes significant economic loss in salmonid aquaculture. We previously detected genetic variation in survival following challenge with Flavobacterium psychrophilum, the causative agent of BCWD in rainbow trout, and a family-based selection program to improve resistance was initiated at the NCCCWA in 2005. In order to understand the genetic architecture underlying variation in disease resistance, we made select crosses in 2007 and 2009 and phenotyped fish using an injection challenge to assess disease resistance. In 2009, fifteen families were created with a predicted F2 or back-cross segregation to major loci based on full-sib family performance of the grandparents and parents. From each family, 200-260 fish were challenged in 4-6 replicates per family. Genome scanning of three families with over 300 microsatellite markers spaced at an average interval size smaller than 10cM along the rainbow trout chromosomes was conducted and major QTL were detected. The QTL will be tested by genotyping of half-sib families and test crosses of fish from this germplasm with un-related germplasm from other rainbow trout broodstocks.