The phylogenetically conserved gene RPBII is frequently used in molecular taxonomy. A number of positions that show intragenomic nucleotide dimorphism were identified in Metschnikowia strains, indicating that the gene may have two copies in their genomes. The translated amino acid sequences were compared and the effect of the dimorphism on the results of a phylogenetic analysis was investigated. The effect of the amino acid substitutions on the folding of the proteins was investigated too. A set of such exchanges were identified, comprising 25 nucleotides exchanges and five amino acid changes. The latter can be assumed to affect the activity of the protein.