Thrips tabaci Lindeman (Thysanoptera: Thripidae), a cosmopolitan pest insect, is subdivided into at least three genetic lineages that have different biological characters, such as reproductive mode and resistibility to insecticides. Since the lineages are discriminated only by mitochondrial DNA, there is a possibility of gene flow among lineages at the genomic level. Nine polymorphic microsatellite loci were newly isolated from the taxon. Moderate to high levels of polymorphism were observed, with numbers of alleles ranging from 6 to 12 in 51 individuals. The mean observed and expected heterozygosities ranged from 0.1373 to 0.3725 and 0.5381 to 0.7748, respectively. Contrary to the expectation under Hardy-Weinberg’s equilibrium, six of the nine loci exhibited a reduction to homozygosities. However, we confirmed that alleles in all the loci were inherited as Mendeilan characteristics. These new loci will be useful to explore discrimination of lineages and population genetics in this species.