A method for detecting, quantifying and differentiating by flow cytometry Brettanomyces spp yeast cells contained in an organic liquid substrate which contains fermentable sugars, whereby a sample of the substrate is taken, optionally diluted, at least a first fluorochrome capable of binding to the DNA of dead and/or live cells is added to the optionally diluted substrate, the sample is irradiated so as to obtain the fluorescence emission of the first fluorochrome and the sample is also irradiated so as to obtain a fluorescence emission of the sample at 670 nm, a biparametric histogram is plotted giving for each point the fluorescence intensity due to the first fluorochrome and the fluorescence intensity emitted at 670 nm, at least a first point cloud is thus-obtained corresponding to a greater fluorescence intensity emitted and detected at 670 nm than that detected for the other points, wherein the points of the first cloud correspond to the Brettanomyces spp cells and the number of Brettanomyces spp cells is optionally enumerated by counting the points of the first cloud.