Evidence is reported for balancing selection acting on variation at major histocompatibility complex (MHC) in wild populations of brown trout Salmo trutta . First, variation at an MHC class I ( satr‐uba )–linked microsatellite locus ( mhc1 ) is retained in small S . trutta populations isolated above waterfalls although variation is lost at neutral microsatellite markers. Second, populations across several catchments are less d...