The brewing yeast, Saccharomyces, carlsbergensis, is allopolyploid, derived from two diverged genomes. To obtain information about the possible origin of this yeast, we cloned two different S. carlsbergensis MET2 genes (encoding homoserine acetyltransferase). One has a nucleotide (nt) sequence identical or very similar to MET2 of Saccharomyces cerevisiae. The other has a different sequence, but was functional in S. cerevisiae. This allele was sequenced and revealed a coding region of 486 amino acids (aa). The nt sequence of the coding region showed 82% homology to S. cerevisiae MET2, while the derived aa sequences were 94% identical. Hybridization experiments to genomic DNA of different yeast strains revealed that the divergent MET2 gene had higher sequence homology to segments from type strains of S. monacensis, S. bayanus and S. uvarum than to MET2 from S. cerevisiae. Sequencing of 330 bp of a PCR-amplified fragment of MET2 from these organisms shows that the non-S. cerevisiae-like sequence from S. carlsbergensis is identical to the corresponding sequence in S. monacensis, while it is 93% homologous with S. bayanus and S. uvarum. Our results are consistent with the proposal that S. carlsbergensis originated as a hybrid between S. monacensis and S. cerevisiae. The complete identity of the MET2 fragments from S. monacensis and the S. carlsbergensis-specific MET2 allele suggests that the hybridization must have been a quite recent event.