We tested the utility of 18 previously characterized Aphis spp. microsatellite loci for polymorphism and differentiation among populations of the soybean aphid, Aphis glycines. Loci were chosen from a closely related species (Aphis gossypii) and a more distantly related species (Aphis fabae). We found nine loci to be polymorphic among Korean and North American populations. Overall expected heterozygosity was moderate (average: 0.47; range: 0–1), although populations substantially differed in deviations from Hardy-Weinberg equilibrium. These loci will be valuable in characterizing population differentiation, migration and adaptation in an economically important pest of soybeans.