The determination of geographical origin is a demand of the traceability system of import-export food products. For this purpose, molecular techniques employing 16S, 26S rDNA profiles generated by PCR-DGGE (polymerase chain reaction - denaturing gradient gel electrophoresis) were used to detect the variation in microbial community (bacteria, yeast) structures of Pangasius fish from Viet Nam harvested in different aquaculture farms and during different seasons and two fruits Physalis from Egypt and mandarins from Spain and Morocco. In Physalis case, ecology of yeasts was also studied for the same purpose. Bacterial band profiles of fish and mandarins, and yeast band profiles of Physalis were specific for each location and could be used as a bar code to certify the origin of fish and fruits. This method is a new traceability tool which provides food with a unique biological bar code and makes it possible to trace back the food to their original location.