[Objectives]  The mitochondrial genome has been widely used in studies of insect phylogeny. We conducted a comparative analysis of the mitochondrial genomes of two aphid species in the Chaitophorinae and used these data to reconstruct the phylogenetic relationship between these species. [Methods]  We used a combination of long and short PCR methods to sequence the mitochondrial genomes of Periphyllus acerihabitans Zhang and Chaetosiphella stipae Hille Ris Lambers, 1947. We sequenced and predicted tRNA secondary structures using the online tRNAscan-SE Search Server. We also used BI and ML approaches to reconstruct the phylogenetic relationships between 12 Aphididae species based on variation in protein-coding genes sequences (PCGs). [Results]  We obtained about 94% of the mitochondrial genome sequences of the two aphid species. That of P. acerihabitans was 14 908 bp long, with a control region length of 1 205 bp, whereas that of C. stipae was 13 893 bp long with a control region length of 609 bp. The mitochondrial genome of these two aphids each has 33 genes, including 13 almost complete PCGs (nad5 incomplete), 18 tRNA and 2 rRNA. A ka/ks analysis indicates that C. stipae evolved faster than P. acerihabitans. The organization of the mitochondrial genome, gene order, nucleotide composition, codon usage, and secondary tRNA structures, were similar in both species. The associated phylogenetic analysis supports the monophyly of the Chaitophorinae and Aphidinae, because of the basal relationship of the Chaitophorinae within Aphididae. [Conclusion]  P. acerihabitans and C. stipae have similar mitochondrial genomes, which are also mostly similar to those previously reported for other aphids. There are, however, differences in the control regions in each species which may lead to variation in size of the whole genome. Phylogenetic reconstruction supports the monophyly of the Chaitophorinae and Aphidinae. These results will benefit reconstructing the phylogeny of all aphid species.