A method was developed for fusing chromosomes in Saccharomyces cerevisiae by employing the site-specific recombination system of pSR1, a circular DNA plasmid originating from Zygosaccharomyces rouxii, and a conditional centromere. 58-bp DNA fragments bearing the specific recombination sites (RSs) of pSR1 were inserted in the subtelomeric regions of chromosomes I (231 kbp) and XI (666 kbp) of a host strain in which chromosome I had a conditional centromere, i.e., a centromere whose function can be switched off upon induction of the GAL1 promoter placed beside it. The resultant cells were then transformed with a plasmid bearing the R gene of pSR1 encoding the site-specific recombination enzyme connected downstream of the GAL1 promoter. When the transformant was cultivated in a galactose medium, the site-specific recombination enzyme catalyzed recombination between the two RSs inserted in the subtelomeric regions of chromosomes I and XI, generating a dicentric fusion chromosome (863 kbp) and an acentric one (46 kbp). Simultaneously, the function of the conditional centromere on the resultant fusion chromosome was switched off. The acentric chromosome was lost during cultivation, resulting in a yeast strain having 15 chromosomes. The fused chromosome was mitotically stable; its rate of loss was (1.68+/-0.24) x 10(-5) per cell division compared to a rate of loss of (1.09+/-0.54) x 10(-5) per cell division for a normal chromosome I.