Introduction. Consumption of citrus fruits and their juice has strongly grown in the last few decades. However, at the present time, the traceability of these fruits is only documentary. In case of doubt or fraud, no standardized analysis makes it possible to discriminate or determine the geographical origin of culture of the fruit. Materials and methods. A method of bacterial ecology, PCR-DGGE, was used to characterize the bacterial flora of clementines imported into France from Spain and Morocco in order to show that there is a relation between the bacterial communities of the fruits and their geographical origins. The principle rests on the determination of specific biological markers for a given region. Protocols of microbial extraction and DNA amplification were optimized. Results. DGGE profiles analyzed by multivariate analysis permitted us to distinguish microbial communities from different origins. Conclusion. We propose the PCR-DGGE method as a new tool for traceability that provides citrus products with a unique bar code and makes it possible to trace back the citrus fruit to their original location.