Flolocyclic individuals of the aphid Rhopalosiphum padi reproduce by cyclical parthenogenesis, while anholocyclic individuals are obligate parthenogens. Although admixed on the secondary hosts in summer, holocyclic and anholocyclic populations occur separately on the primary and secondary hosts during winter and spring. In this study, we compared the genetic diversity and population structure of holocyclic and anholocyclic populations collected in spring in the northern half of France. We also analysed the genetic composition of summer populations of R. padi on its secondary hosts. In spring, holocyclic populations were in Hardy-Weinberg equilibrium at individual loci and had a relatively high genotypic diversity. Conversely, anholocyclic populations deviated from Hardy-Weinberg equilibrium and often consisted of a single clone. Moreover, these populations showed very low mean heterozygosities compared with holocyclic populations. Analysis of summer populations suggested that in regions with cold winters, summer populations were largely recruited from holocyclic clones, whereas in areas with mild winters, summer populations were mainly derived from anholocyclic clones. These results permit an assessment of the geographical distribution of the two modes of reproduction on a large scale. The reasons for the diminished heterozygosity of anholocyclic populations are also discussed in relation to the mechanisms which may induce transitions to asexuality in aphids.