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Drought is predicted to be more frequent, prolonged, and intensive in many areas around the globe under future warming scenarios, which can have significant impacts on aphids in different agricultural systems. However, studies on the genetic structuring process underlying changing aphid biology and ecology under drought are rare. To address the issue, we collected the wheat aphid, Sitobion avenae (Fabricius) (Hemiptera: Aphididae), clones from moist, semiarid, and arid areas of northwestern China and genotyped them with microsatellite markers. We found 59 multilocus genotypes from 235 collected individuals. Populations of S. avenae in different areas showed a moderately high level of genetic diversity. F IS values across all loci in all S. avenae populations were found to be negative, indicating heterozygote excess and prevalent parthenogenesis in our sampling areas. The appearance of a relatively large number of unique genotypes in Yulin provided evidence for the existence of sexual reproduction there. Based on Bayesian clustering analyses, the majority of individuals from moist and semiarid areas belonged to one cluster, whereas most individuals from arid areas fell into another cluster. We found little population structure of S. avenae in moist or semiarid areas, but a significant population structure for arid areas. Significant amounts of migration of S. avenae were found between our sampling areas although the migration was asymmetric between areas. This study provides insights into the genetic diversity, divergence, and structure of aphid populations under drought, as well as valuable information for improving aphid management strategies in drought-inflicted areas under future warming scenarios.