Since 2005, the European regulation 178/2002 imposes the traceability process of foodstuffs (Article 17). In practice, traceability of foods is mainly done at the administrative level, and the use of analytical tools is rare. Previous studies have demonstrated that microbial ecology analyses at the molecular level (such as PCR-DGGE) could be used to provide food with a unique biological signature that could be linked to the geographical origin of food. The aim of this project was to use this approach to test whether we could differentiate organic from conventional foods, in order to improve the traceability of such products. The hypothesis was that the different processes applied to different types of agriculture have an influence on the microorganisms that are present on foods. In our study, analysis of yeast and bacterial rDNA DGGE profiles revealed that yeast and bacteria communities were specific of organic nectarines and could discriminate organic fruits from conventional or sustainable fruits. We showed also that microbial ecology structure (yeast and bacteria) is specific of the production mode. Some species, well identified could be used as biological markers to certify the origin as well as the mode of production of foodstuff. We proposed this analytical tool as a first step to control and authentify organic food.