Infectious hematopoietic necrosis (IHN) is a rhabdoviral disease of salmonid species. Single strand conformation polymorphism (SSCP) was used to identify association between DNA polymorphism of the major histocompatibility complex (MHC) class II beta-chain intron and IHN virus (IHNV) resistance in backcrosses of rainbow trout (Oncorhynchus mykiss) and cutthroat trout (O. clarki). Association was significant (P=0.024) in four half-sib families from one sire (number 2), but not among half-sibs from another sire (number 1). DNA sequencing analysis revealed that the polymorphism originating from sire 1 is the result of a single base substitution. Sire 2 polymorphism was caused by three different base substitutions. The source of the susceptible allele appears to be from cutthroat trout and not from the rainbow trout population used to produce the hybrids. The results suggest that MHC polymorphism can contribute to linkage and association studies of immunity to infectious diseases in rainbow trout.