The cereal aphids, Rhopalosiphum maidis (Fitch) and Rhopalosiphum padi (L.) (Hemiptera: Aphididae), are serious pests of maize, Zea mays L., globally. Basic information about the genetic structure of these aphids is unknown. We, therefore, estimated the genetic diversity and genetic flow from partial fragments of the mitochondrial cytochrome oxidase I gene collected from different geographic populations of aphids throughout the Songliao Plain of northeastern China. Our analysis of a 425-bp sequence on 297 R. maidis and 287 R. padi individuals revealed 17 and 3 variable sites, respectively. Fifteen haplotypes were obtained among the R. maidis populations, and only haplotype RM1 was shared. Three shared haplotypes were obtained among the R. padi populations. No obvious geographical trends were detected based on the haplotype network and neighbor-joining tree. Relatively low haplotype diversity indices were observed in the R. maidis populations (haplotype diversity [Hd] = 0.14207, average number of nucleotide differences [K] = 0.17340, and nucleotide diversity [Pi] = 0.00041), whereas relatively high haplotype diversity indices were observed in the R. padi populations (Hd = 0.53249, K = 1.46614, and Pi = 0.00345). There was moderate gene flow (number of migrants [Nm] = 2.33) among R. maidis populations, but there was low gene flow (Nm = 0.82) among R. padi populations. Analysis of molecular variance showed high genetic differentiation within populations. Genetic distance and geographic distance were not significantly associated according to the Mantel test. The results suggest that the difference in the aphids' existence strategies has resulted in a different mitochondrial evolution pattern in the Songliao Plain region, and they provide a foundation for accurately forecasting systems against this pest.