Pterochloroides persicae (Cholodkovsky) is an aphid species belonging to the subfamily Lachninae that uses different members of Rosaceae (specially Prunus spp.) as hosts. Partial sequences from the mitochondrial cytochrome c oxidase 1 (COI) and the nuclear long-wave opsin genes were obtained for approximately 100 P. persicae aphid individuals sampled from 34 colonies collected mainly in Tunisia and other Mediterranean locations. The variability found at the mitochondrial locus revealed the presence of two maternal haplotypes in the studied area that differed in a single nucleotide. The nuclear gene analyzed, however, failed to reveal any variability in this species. The variability found at the COI locus was related to the season of aphid sampling and with the site of feeding, with haplotype I mostly detected in samples collected in spring and summer on trunks and branches and haplotype II only detected in aphids collected in autumn on roots. The observed pattern of molecular variation suggests the presence of two clonal races of P. persicae coexisting in the studied area differentially adapted to conditions prevalent in the alternative seasons and/or to different feeding sites.