Bacterial cold water disease (BCWD) causes significant economic loss in salmonid aquaculture. Using microsatellites genome scan we have previously detected highly significant QTL with major effect on the phenotypic variation of survival following challenge with Flavobacterium psychrophilum (Fp), the causative agent of BCWD in rainbow trout (Oncorhynchus mykiss). In this study, we used selective genotyping of SNPs from SbfI restriction-site associated DNA (RAD) sequence data from two pedigreed families to validate the major QTL from the previous work and to detect new QTL.