Single nucleotide polymorphisms (SNPs) on rainbow trout chromosomes Omy16 and Omy17 are associated with a lower parasitic load and delayed-time-to-death following exposure to the parasitic ciliate Ichthyophthirius multifiliis causing white spot disease (WSD). We have evaluated the application of two quantitative trait loci (QTL) represented by two of these SNPs for practical breeding purposes. Homozygous males served as parent fish securing offspring with at least one allele (heterozygous and homozygous fish) associated with higher resistance (QTL fish). We measured the infection levels and time to morbidity/mortality in QTL fish and in non-QTL fish (male parent fish negative for the SNPs) following exposure to infective theronts. We conducted hexaplicate challenge trials (common garden experimental set-up in each tank) and recorded the development of trophonts (white spots) in the fish epidermis and associated morbidity in all six fish tanks and in both fish groups. QTL fish showed a significantly lower infection and delayed development of WSD morbidity. Analyses of SNP locations on the trout chromosomes Omy 16 and Omy 17 may in the future indicate genes associated with higher natural protection. Evidence points at immune factors, physiological functions, mucus production and regulatory elements (lncRNA and pseudogenes).