In this paper new primers, annealing to the ITS2 region, were used to obtain a PCR product that was subsequently subjected to Temperature Gradient Gel Electrophoresis (TGGE) analysis. The PCR-TGGE method performed was able to distinguish Saccharomyces cerevisiae and S. paradoxus and distinguish between strains of S. cerevisiae. Direct analysis of S. cerevisiae and S. paradoxus ecology in musts were also performed.