The Asian long-horned beetle (ALB), Anoplophora glabripennis (Motschulsky) (Coleoptera: Cerambycidae: Lamiinae), is a wood-borer and polyphagous xylophage that is native to Asia. It infests and seriously harms healthy trees, and therefore is a cause for considerable environmental concern. The analysis of population genetic structure of ALB and sibling species Anoplophora nobilis (Ganglbauer) will not only help to clarify the relationship between environmental variables and mechanisms of speciation, but also will enhance our understanding of evolutionary processes. However, the known genetic markers, particularly microsatellites, are limited for this species. SSRLocator software was used to analyze the distribution and frequencies of genomic simple sequence repeat (SSR), to infer the basic characteristics of repeat motifs, and to design primers. We developed SSR loci of 2–6 repeated units, including 10,650 perfect SSRs, and found 140 types of repeat motifs. A total of 2621 SSR markers were discovered in ALB whole-genome shotgun sequences. 48 pairs of SSR primers were randomly chosen from 2621 SSR markers, and half of these 48 pairs were polymorphic containing 4 di-, 7 tri-, 2 tetra-, and 11-hexamer SSRs. Four populations test the effectiveness of the primers. These results suggest that our method for whole-genome SSR screening is feasible and efficient, and the SSR markers developed in this study are suitable for further population genetics studies of ALB. Moreover, they may also be useful for the development of SSRs for other Coleoptera.