Increasing damage of pests in agriculture and forestry can arise both as a consequence of changes in local species and through the introduction of alien species. In this study, we used population genetics approaches to examine population processes of two pests of the tree‐of‐heaven trunk weevil (TTW), Eucryptorrhynchus brandti (Harold) and the tree‐of‐heaven root weevil (TRW), E. scrobiculatus (Motschulsky) on the tree‐of‐heaven across their native range of China. We analyzed the population genetics of the two weevils based on ten highly polymorphic microsatellite markers. Population genetic diversity analysis showed strong population differentiation among populations of each species, with F ST ranges from 0.0197 to 0.6650 and from −0.0724 to 0.6845, respectively. Populations from the same geographic areas can be divided into different genetic clusters, and the same genetic cluster contained populations from different geographic populations, pointing to dispersal of the weevils possibly being human‐mediated. Redundancy analysis showed that the independent effects of environment and geography could account for 93.94% and 29.70% of the explained genetic variance in TTW, and 41.90% and 55.73% of the explained genetic variance in TRW, respectively, indicating possible impacts of local climates on population genetic differentiation. Our study helps to uncover population genetic processes of these local pest species with relevance to control methods.