The complete mitochondrial genome of global Diuraphis noxia populations was characterized using NextGen sequencing, and was found to be 15 721 bp in size and consisting of 38 genes typically found within most insects. Single nucleotide polymorphism (SNP) analyses of the genomes of nine populations revealed 125 SNPs in the protein coding genes with the majority of the SNPs occurring in the ND genes, and the least in the ND4L gene. Low SNP variant frequency was also found for the atp6 and atp8 genes, which differed from other reports in the Hemiptera, and may point towards increased importance of these genes in aphid fitness.