A total of 32 yeast strains belonging to four non-Saccharomyces species associated with winemaking was characterized by different molecular techniques. The PCR amplification of 18S rRNA-coding DNA and nontranscribed spacer, followed by restriction analysis with the endonucleases HaeIII and MspI, and PCR fingerprinting with microsatellite primers (GAC)(5) and (GTG)(5) were used. The methods used provided species-specific profiles and proved to be fast and reliable for monitoring the evolution of the four non-Saccharomyces yeast populations throughout wine fermentation.