Microsatellites markers were used to characterise 44 Prunus rootstocks from different species. These included Peach-based rootstocks (P. amygdalo-persica, P. persica x P. davidiana), Myrobalan plums (P. cerasifera), Marianna plums (P. cerasifera x P. munsoniana), and Slow growing plums (P. insititia, P. domestica, P. domestica x P. spinosa). Major differences were observed among the main groups. Preliminary results showed that these rootstocks were clustered in three different groups according to their known pedigrees: Peach-based rootstocks, Fast growing plums (Myrobalan-Marianna group) and Slow growing plums (P. insititia and P. domestica). We should include more microsatellites to measure the genetic diversity within the different groups.