Using Atlantic salmon (Salmo salar) as a model system, we investigated whether 18 microsatellites tightly linked to immune-relevant genes have experienced different selection pressures than 76 loci with no obvious association with immune function. Immune-relevant loci were identified as outliers by two outlier tests significantly more often than nonimmune linked loci (22% vs. 1.6%). In addition, the allele frequencies of immune relevant markers were more often correlated with latitude and temperature. Combined, these results support the hypothesis that immune-relevant loci more frequently exhibit footprints of selection than other loci. They also indicate that the correlation between immune-relevant loci and latitude may be due to temperature-induced differences in pathogen-driven selection or some other environmental factor correlated with latitude.