The sequence variation of three exons of the major histocompatibility complex (Mhc) was examined in a lake whitefish Coregonus sp., population from the Swiss lake of Hallwil. DNA sequences from the Mhc class I A1, A2 and class 11 B1 exons, corresponding to the alpha1, alpha2 and pr domains of the Mhc. glycoproteins, were obtained by the polymerase chain reaction followed by cloning and sequencing. The numbers of variable sequences detected For each exon were 15 (A1), 11 (A2) and 20 (B1). Levels of nucleotide similarity ranged from 82 to 99% For the A1 exon, 58-96% for the A2 and 88-99% for the B1 exon. At the A1 and B1 exons, the nonsynonymous substitution rates (dn) exceeded synonymous substitution rates (ds) greatly within the peptide binding regions, indicating the effect of balancing selection. Sequence diversity at the A2 exon did not seem to be maintained by balancing selection (ds>dn). Phylogenetic comparison of whitefish Mhc sequences with sequences from other salmonid species and more distantly related teleosts indicated shared ancestral (trans-species) polymorphism.