Infectious hematopoietic necrosis (IHN) is a rhabdoviral disease of salmonid species. Initial observations suggested that cutthroat trout ( Oncorhynchus clarki) and hybrids of rainbow trout ( Oncorhynchus mykiss) and cutthroat trout are significantly less susceptible to IHN virus (IHNV) than rainbow trout. Sixteen full-sib families of backcross progeny (female rainbow×male hybrid) were produced and three replicates per family were challenged with IHNV. DNA fingerprints of mixtures from first mortalities and survivors of the IHNV challenges were compared using two restriction enzymes and 10 multilocus probes. An estimated 98–102 polymorphic loci were screened by the bulked segregant analysis (BSA) of the DNA mixtures. Thirty-three multilocus RFLP markers differing between first mortalities and survivors were detected. Of 17 tested a significantly higher frequency of two markers was detected among individuals first to die in one family (C2), and another marker was significantly associated with IHNV resistance in family A4.