English Grain Aphid Sitobion avenae(Fab.) is important and migratory aphid species with wide distribution in wheat growing regions especially in Upper and Middle Egypt. Morphological criteria for aphid species identification may be affected by environmental factors. So,eleven geographical populations of S. avenae were collected from different localities of Egypt. Twenty five quantitative morphological characters (morphometric or numeric) were investigated and screened in the collected populations. On the other hand, genetic variations among those populations based on Mitochondrial-DNA COI gene sequencing and quantitative expression by using Real-time PCR (RT-qPCR) were studied. Finally, relatedness among those populations was also concerned on base of morphological or genetic variations among the populations.Ten morphological characters varied significantly among thosepopulations; however populationsof El-Gharbia and El-Qaloubia governorates were more related morphologically.Relative amounts of mRNA ranged between 7.720±0.451 to 18.180±0.852 as cycles thresholds (Ct) with high significant difference among those populations where the highest amounts of mRNA were detected in geographical population of Domiata followed by Beni-Suif Governorates.Moreover populations of El-Qaloubia and El-Sharqya Governorateswere more related populations.Gene sequencing of mt-DNA COI in eight geographical populations showed 23 polymorphic sites that pairwise distance comparison among them ranged from 0.9% (difference in 6 nucleotides) to 2.7% (difference in 18 nucleotides). The largest sequence divergence was detected when population of Domiata was compared with populations of El-Sharqya or Kafer El-Shikh, while the lowest divergence was detected between populations of El-Behera and El-Monofia Governorates.