【目的】线粒体基因组分析已被应用于昆虫系统发育研究。本研究以蚜科 Aphididae 重要类群毛蚜亚科物种为代表，测定并比较分析了该类蚜虫的线粒体基因组特征，探讨了基于线粒体基因组信息的蚜虫系统发育关系重建。【方法】以毛蚜亚科三角枫多态毛蚜 Periphyllus acerihabitans Zhang和针茅小毛蚜Chaetosiphella stipae Hille Ris Lambers,1947为研究对象，利用长短PCR相结合的方法测定线粒体基因组的序列，分析了基因组的基本特征；基于在线tRNAscan-SE Search Server搜索方法预测了tRNA的二级结构；基于12个物种（本研究获得的2个物种和10个GenBank上下载的物种数据）的蛋白编码基因(PCGs)序列，利用最大似然法和贝叶斯法重建了蚜科的系统发育关系。【结果】两种毛蚜均获得了约94%的线粒体基因组数据，P. acerihabitans获得了14908 bp，控制区为1205 bp；C. stipae获得了13893 bp，控制区为609 bp。两种毛蚜同时获得33个基因，包含接近完整的13个蛋白编码基因(PCGs)（nad5不完整），18个tRNA，2个rRNA基因；ka/ks值表明，C. stipae的进化速率更快。从基因组组成、基因排列顺序、核苷酸组成分析、密码子使用情况、tRNA二级结构等特征来分析，两种蚜虫线粒体基因组基本特征相似。系统发育重建结果表明毛蚜亚科、蚜亚科的单系性得到了支持，毛蚜亚科位于蚜科的基部位置。【结论】两种毛蚜线粒体基因组的基本特征相似，符合蚜虫线粒体基因组的一般特征，两种线粒体基因组的长度差异主要来自控制区长度的不同；系统发育重建支持毛蚜亚科与蚜亚科的单系性，毛蚜亚科位于蚜科较为基部的位置。研究结果为蚜虫类系统发育重建提供了参考。“,”[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 33genes, 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.