The aim of this work was to develop a method for authenticity control of organically grown orange fruits. Due to the different kinds of nitrogen fertilization of the soil in organically and conventionally managed farms, the study tried to verify the possibility to differentiate Navelina and Tarocco orange fruits obtained by these production systems through the detection of markers linked to nitrogen metabolism. In addition to the classic quality parameters, total nitrogen (N) and synephrine contents in juice and (15)N/(14)N isotope ratio (expressed as delta(15)N per thousand) in proteins of pulp and amino acids of juice were determined. The results obtained indicated that total N and synephrine contents were significantly higher in conventional fruits, whereas the delta(15)N per thousand values were higher in the organic ones. The new markers identified in this research by linear discriminant analysis of the data may constitute a useful tool to differentiate organic citrus fruits or juices from conventional ones.