Sitophilus oryzae (Coleoptera: Curculionidae) and Sitophilus zeamais (Coleoptera: Curculionidae) are major insect pests of farm-stored grains in China. Moreover, their respective distribution and prevalence are not yet assessed for grain storage facilities in China. The two species are often difficult to identify by morphology because they are immature or their presence is only evident from fragments. Species-specific primers were, therefore, designed based on the cytochrome c oxidase subunit I (COI) of 34 populations found throughout China and three foreign populations. Following the validation of this molecular-based approach for species identification, the distribution of the two species in China was determined from 68 different grain storage facilities. The results indicate that S. zeamais is prevalent throughout the country whereas S. oryzae is mainly present in the south and the center of China. It is believed that this distribution pattern is in function of ecological adaptation, mostly determined by temperature and the grain species. This is the first report of its kind, demonstrating the distribution of S. zeamais and S. oryzae in grain storage facilities throughout China and analyzed by species-specific primers of COI.