In this study, the genetic structure of 15 populations of the potato aphid, Macrosiphum euphorbiae Thomas (Hemiptera: Aphididae), from Tunisia was characterized using RAPD markers. Five decameric random primers revealed 113 polymorphic loci that were used to estimate population structure with an average of 22.6 polymorphic bands per primer. Analysis of molecular variance (AMOVA) showed significant (P < 0.001) genetic diversity among populations (78.16 %) rather than within populations (21.84 %) that has been confirmed by Fst and Nm values. A cluster analysis based on genetic distance revealed that the 15 populations were divided into three groups. Populations from the south were differentiated into one group irrespective of host plant, whereas the other populations were distributed between two groups independently of the geographic origin and host plant. These results represent the first evidence for genetic structuring in M. euphorbiae.