In the framework of the 6th PCRD European Project 'CIBEWU', the genetic diversity of Tunisian Citrus rootstocks germplasm was assessed using microsatellite markers (SSR). This work started with a prospection in order to identify the different rootstocks used all over the country, focusing on those which are the most adaptable to abiotic stress (mainly salinity). Sour Orange is by far the most widely used in Tunisia. However, we have also observed other rootstocks in some aged plantations and in southern Tunisia. Our survey has showed that these rootstocks are being used since a long time in the oasis of southern Tunisia and were preferred than Sour Orange by fanners due to their adaptation to the particular conditions of the oasis. We have collected a total set of 206 accessions, on which, 20 SSR markers were performed. This work generated interpretable results for all markers and a total of 121 alleles were revealed. Little variability was observed among Sour Orange (Citrus aurantium L.) rootstocks, while specific alleles were observed for the other rootstocks such as Limes, lemons and oranges. The genetic diversity assessment of the Citrus local rootstocks resources allowed the estimation of the variability either within the Sour Orange and between Sour Orange and the other rootstocks analysed. This work plays a role in the preservation of local resources biodiversity. Prospection, collection and identification, object of this study will avoid the loss of important local resources diversity. Indeed, even if the Sour Orange is threatened by the spread of Citrus Tristeza Virus over the Mediterranean Basin, it constitutes a good local material, very well adapted to local abiotic stress conditions. The Sour Orange diversity with the other local rootstocks form a genetic heritage of great importance for further rootstock breeding project and has to be preserved. (Texte intégral)