The pink stem borer, Sesamia inferens (Walker) (Lepidoptera: Noctuidae), is an important pest of rice in China and other parts of Asia. The wide geographic distribution and broad host range of S. inferens is likely to result in high genetic variability within the species. To better understand the genetic structure and phylogeography of this pest, 30 polymorphic microsatellite loci were developed and characterized by fast isolation by amplified fragment length polymorphism of sequences containing repeats (FIASCO). Our results from two geographic locations (Yangzhou and Guiyang) showed that the polymorphic information content (PIC) ranged from 0.181 to 0.947, with an average of 0.633 (relatively high polymorphism). The number of alleles per locus ranged from 2 to 31, with expected heterozygosities from 0.196 to 0.962 and observed heterozygosities from 0.043 to 1.000. Fourteen loci showed no significant departure from Hardy—Weinberg equilibrium after sequential Bonferroni's correction at least in one population; furthermore, loci CA194 and GT106, GA13 and TG52, GA13 and TG51, CA31 and CA43, GT16 and GT206 showed significant linkage disequilibrium. A preliminary analysis of mutation patterns in microsatellites was undertaken, and three types of microsatellite mutation patterns were described. We conclude that the microsatellite markers described herein will be useful in studying population genetics within S. inferens. Furthermore, some of the microsatellites show high polymorphism and lack null alleles, indicating potential use in the identification of the species, S. inferens.