Arctic charr, a highly plastic salmonid that inhabits the circumpolar region, colonized its current environment after the last glaciation. Recent colonization limits the capacity of many techniques to define and characterize constituent populations. As a novel approach, we used the major histocompatibility (MH) class IIα gene polymorphism as a marker that would characterize the genetic divergence of global Arctic charr populations caused by drift and by local adaptation to pathogens. We were able to detect significant isolation of all the lineages previously defined by mitochondrial DNA sequencing and also isolation of some populations within those groups. We found that most of the polymorphism of the class IIα gene was distributed globally, which indicates ancestral selection; however, in most cases, distinctive allele frequencies and specific haplotypes distinguished each population suggesting that recent selection has also occurred. Although all studied populations showed similar MH class IIα polymorphisms, we also found variation in which particular amino acid positions were polymorphic and which were constant in the different populations studied. This variation provides a greater adaptive capacity for the MH class IIα receptors in Arctic charr and is yet another illustration of the extraordinary plasticity of the species.