This study was undertaken to evaluate the biodiversity of the indigenous Saccharomyces sensu stricto population during traditional vinification processes of Recioto and Amarone wines using molecular typing techniques. In total 109 isolates, collected from eight wineries during spontaneous fermentations, were identified and characterised by conventional tests and by molecular methods, i.e. PCR fingerprinting using the primer (GTG)5, mtDNA restriction and karyotype analyses. Sixty per cent of the isolates were assigned to Saccharomyces bayanus var. uvarum and 40% to Saccharomyces cerevisiae. A succession between S. bayanus var. uvarum, which dominated the first fermentation, and S. cerevisiae, which appeared after the wine drawing-off operation, was observed during a traditional Amarone winemaking. An extensive polymorphism was found between the isolates, however a few specific genetic biotypes prevailed in the different wineries. This ecotaxonomic survey constitutes a basic step to safeguard and exploit the oenological potential of the yeast biodiversity in the Recioto and Amarone wine ecosystems. Such biodiversity could be further explored to correlate the genetic patterns of the isolates with oenologically useful characteristics, with the ultimate goal to carry out selection programmes of typical strains of the Valpolicella area