This study explored the use of the gene encoding the β subunit of the major histocompatibility (MH) receptor as a population marker in Arctic charr Salvelinus alpinus. The use of this polymorphic marker allowed differentiation of the S. alpinus lineages previously defined using mitochondrial DNA (mtDNA) but also allowed differentiation between the populations studied within those lineages. The majority of the variation observed here occurred prior to the last glaciation event. Nevertheless, all S. alpinus populations were differentiated using both MH Class II β (mh-IIβ) sequences and allelic frequencies. The fact that all the populations studied presented high rates of non-synonymous: synonymous substitutions and high levels of interpopulation variation, suggested mh-IIβ as an ideal marker to assess differentiation among S. alpinus populations in ways that may represent divergence both by genetic drift and natural adaptation to the local environment.