Traceability of fruits is only documentary. In case of doubt or fraud, no standardized analysis makes it possible to trace back the origin of the fruit. The aim of this study is to apply PCR-DGGE method to analyze in a unique step all the yeasts present on the fruit to create the linkage between yeast communities and their geographical origins. PCR-DGGE is a method of yeast ecology which was used to characterize all the yeast flora of three species of Physalis fruit (Physalis ixocarpa Brot, Physalis pruinosa L, Physalis peruviana L) from Colombia, Egypt, Uganda, Madagascar. DGGE fingerprints analyzed by multivariate analysis permitted to distinguish different fruit origins by their yeast communities. PCR-DGGE method is then proposed as a new traceability tool which provides to the fruits in general and Physalis in particular with a unique bar code for each country by using 26S rDNA fingerprinting of yeasts.