Introduction. Consumption of Physalis fruits is quite recent and theproducts are poorly known among consumers. This plant has been known for a long time as anornamental in Europe, for at least 200 years. Traceability is increasingly becomingimportant across the agri-food industry; however, at the present time, the traceability ofthis fruit is only documentary. In case of doubt or fraud, no standardized analysis candetermine the geographical origin of the fruits. Materials and methods. Inorder to discover the relationship between the fungal communities of the fruit and theirgeographical origins, 28S rDNA-PCR-DGGE was used to analyze the variation in fungalcommunities in three species of Physalis fruit (Physalis ixocarpa Brot.,Physalis pruinosa L. and Physalis peruviana L.) fromEgypt, Uganda and Colombia. Results. Denaturing Gradient Gel Electrophoresis(DGGE) fingerprints of 28S ribosomal DNA (28S rDNA) analyzed by multivariate analysiscould distinguish different fruit origins by their fungal communities.Conclusion. We propose the PCR-DGGE method as a new traceability tool whichprovides fruit in general, and Physalis in particular, with a unique barcode for eachcountry by using 28S rDNA fingerprinting of fungi.