In the present study, we investigated six Saccharomyces strains (two parental strains from different species and their four hybrids). In order to prove the possibility that horizontal gene transfer can take place through interspecies hybridisation in lower eukaryotes, we showed that the hybrids contained complete genomes from the hybridising species but their alloploid genomes were unstable and prone to undergo segregation. In the analysis we used classical methods (assimilation and fermentation tests, random spore analysis) and molecular methods (PCR-RFLP and electrophoretic karyotyping).