The study of the fermentation process in the Alicante region allowed us to conclude that adverse climatic conditions could be responsible for deficient wine-making with serious problems arising fermentations, usually causing incomplete fermentation. In order to avoid these problems, we selected a Saccharomyces cerevisiae strain, namely T73, isolated in the same Alicante region, to be used to perform controlled fermentations. The use of selected strains in the wine-making process requires the development of characterization techniques that can clearly differentiate between the inoculated strain and the wild strains present in the musts. In order to differentiate strains present in the wine ecosystems, an extensive survey of different methods of yeast strains identification has been carried out. However, these techniques are very complex to be used in industry. For this reason, we have developed a new, simple, inexpensive and rapid method based on mitochondrial DNA restriction analysis. This technique was applied to the control of wine fermentations conducted by active dry yeasts. This molecular approach allows us to understand the role of the inoculated dry yeast strain and that of the natural S. cerevisiae flora during wine fermentation.