We describe a rapid method developed to identify yeast species commonly found during cheese ripening. It is based on the isolation of species-specific sequences and their hybridization with coarse preparations of genomic DNA. Several strategies were followed for the construction of probes: PCR amplification of sequences available in databases, random cloning of genomic DNA fragments, specific RAPD fragments and PCR-amplified ribosomal DNA fragments. After validation, the probes were applied to the characterization of 400 yeast strains isolated from various French cheeses. Since the strains had been previously identified with classical diagnostic tests, we were able to compare molecular and conventional identification. In addition, the specific probes for one of the species, Debaryomyces hansenii, were used successfully in colony hybridization experiments. The probes developed here proved to be very useful for the screening of large yeast collections and for the assessment of biodiversity within the yeast flora in cheese.