We used a quantitative genetics approach and estimated broad sense heritability (h²b) of myxospore count and the number of genes involved in myxospore formation to gain a better understanding of how resistance to Myxobolus cerebralis, the parasite responsible for whirling disease, is inherited in rainbow trout Oncorhynchus mykiss. An M. cerebralis-resistant strain of rainbow trout, the German Rainbow (GR), and a wild, susceptible strain of rainbow trout, the Colorado River Rainbow (CRR), were spawned to create 3 intermediate crossed populations (an F1 cross, F2 intercross, and a B2 backcross between the F1 and the CRR). Within each strain or cross, h²b was estimated from the between-family variance of myxospore counts using full-sibling families. Estimates of h²b and average myxospore counts were lowest in the GR strain, F1 cross, and F2 intercross (h²b = 0.34, 0.42, and 0.34; myxospores fish⁻¹ = 275, 9566, and 45780, respectively), and highest in the B2 backcross and CRR strain (h²b = 0.93 and 0.89; myxospores fish⁻¹ = 97865 and 187595, respectively). Comparison of means and a joint-scaling test suggest that resistance alleles arising from the GR strain are dominant to susceptible alleles from the CRR strain. Resistance was retained in the intermediate crosses but decreased as filial generation number increased (F2) or backcrossing occurred (B2). The estimated number of segregating loci responsible for differences in myxospore count in the parental strains was 9 ± 5. Our results indicate that resistance to M. cerebralis is a heritable trait within these populations and would respond to either artificial selection in hatcheries or natural selection in the wild.