Variation in antipredator behavior may partially explain the survival differences seen between wild and hatchery trout and salmon. Antipredator behavior is thought to change during the domestication process, along with other traits. Investigations of antipredator behavior could benefit conservation efforts and supplementation programs. Our goal was to characterize the antipredator behavior in clonal rainbow trout lines derived from either wild or hatchery populations and identify genetic loci associated with variation between lines. We identified several behaviors that varied between clonal lines and QTL for several behavioral and size traits. Characterizing genetic variation underlying these behaviors may prove valuable in future conservation efforts by enabling monitoring of allele frequencies of loci affecting predation in wild populations.