The green oak leafroller moth, Tortrix viridana Linnaeus, 1758 (Lep. Tortricidae) is one of the key pests on Quercus spp. The larval instars of the moth feed on the developing buds and the leaves and cause oak trees to be leafless completely, significantly damaging the oak forest of northwestern Iran each year. The genetic differences in the host plant associated populations of oak leafroller moth have been assessed in the oak forests of northwestern Iran using inter-simple sequence repeat markers (ISSR). In this study 171 specimens representing nineteen populations feeding on various oak tree species including Quercus branti Lindl. 1840, Quercus infectoria Oliv. 1801 and Quercus libani Oliv. 1801 were investigated. Results indicated that populations related to Q. libani had the highest genetic diversity, while populations related to Q. branti and Q. infectoria had lower genetic diversity. Assessment of genetic structure of the populations showed that higher diversity was demonstrated in intrapopulations (92%) than interpopulations (8%) geographically, while strongly significant host-associated differentiation was also indicated by Approximate Bayesian Computation analyses among populations, with major clusters corresponded to the three species of host plants. These findings revealed that the host plant association can have a stronger effect on the genetic variations among the populations of T. viridana than the geographical barriers.