The vinegar fly, Drosophila suzukii (Diptera: Drosophilidae), is a recent invader in North America that has become a serious threat to small fruit production. It was first detected in California in 2008 and in Washington state in 2009. In this study, D. suzukii populations from the area of the original detection on California's central coast and from eastern Washington, the United States, were sampled over a 3-year period to determine genetic variation in both using microsatellite markers. Six different loci were successfully amplified and included in the analysis. These loci included nanos, elf1, antennapedia, mastermind, z600, and tenA. The population from eastern Washington was highly monomorphic with one locus, mastermind, having multiple alleles. There was greater genetic variation in the coastal California population with all loci having multiple alleles, with the exception of tenA. Owing to the relatively low levels of genetic variation in the eastern Washington population compared with the coastal California population, it appears that the D. suzukii population in the eastern Washington region has undergone a significant bottleneck.