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The present study examined whether the mutualistic relationship between the aphid Tuberculatus quercicola (Matsumura) (Homoptera: Aphididae) and the attending ant Formica yessensis Forel (Hymenoptera: Formicidae) has had any mutual effects on the microgeographical genetic population structure of both partner species. The aphids and the attending ants were collected in June, August, and October 2004 from six trees of the Daimyo oak Quercus dentata Thunberg (Fagales: Fagaceae) and were genotyped using microsatellite loci. Significant genetic differentiation was detected among T. quercicola populations on the respective trees across seasons (an average of pairwise FST = 0.183). Similarly, significant genetic differentiation was found among populations of F. yessensis that attended aphid colonies on the respective host trees, though the averages of pairwise FST were lower (an average of pairwise FST = 0.070). An analysis of molecular variance and two-way ANOVA detected a significantly large genetic difference between spring and summer samples in F. yessensis but not in T. quercicola, indicating that changes in genetic composition occurred in the F. yessensis colony. In spite of a drastic seasonal change in the genetic difference in F. yessensis, principle coordinate analysis showed that the relative position among the six populations was maintained from spring to summer, suggesting that the tree where honeydew was available for a long time was occupied by F. yessensis over the same period and that the honeydew sources were inherited at the level of the ant colony. It is hypothesized that the suitability of host trees for the aphid T. quercicola may have an affect on the genetic structure of the attending ant F. yessensis. Within a colony of aphids, clonal diversity decreased significantly as the season progressed. The reduction in clonal diversity may be due to an increase in identical genotypes by parthenogenesis or selective pressure from host plant deterioration.