The weevils Eucryptorrhynchus brandti (Harold) and E. scrobiculatus (Motschulsky) are two pests of the tree of heaven, Ailanthus altissima. They usually co-occur on their host tree. However, these two species have a niche separation with different eggs-laying locations and larvae-feeding parts on the tree. Here, we characterized the distribution of microsatellites in the genome and developed genome-wide microsatellite markers shared between these two weevils. A total of 12,524 and 11,030 potential microsatellites were identified for E. brandti and E. scrobiculatus, respectively. Microsatellites with AT, TA, AC, TG, CA repeat motifs were most common for both species. We designed primers universal for two weevils and developed 14 loci with high amplification efficacy and polymorphism. We validated these microsatellite markers in three populations of each species. In E. brandti, the observed and expected heterozygosity for the genotyped loci ranged from 0.17–0.24 and 0.44–0.54; in E. scrobiculatus, the above values ranged from 0.06–0.18 and 0.18–0.27. Based on the developed microsatellite markers, we found that populations of both weevils have a clear pattern of genetic differentiation. Our study provides valuable genetic markers for ecological, genetic, and evolutionary study of these two weevils.