The application of nuclear and mitochondrial gene sequences in the molecular phylogenetics of Aphididae (Hemiptera) is summarized, with a special focus on the scientific problems which they can resolve. Among the nuclear genes, sequences of EF-1α are used most widely, and they are fit for studying the phylogenies at genus or higher levels; nuclear rDNAs are used less in aphids’ phylogeny analysis, LWO is a new marker developed in aphids, and both of them are applicable for higher-level taxa above family. Among the mitochondrial genes, the most often used markers are COⅠ/COⅡ. 12S rDNA/16S rDNA, ND1, Cyt b and F-ATP6 are also used in Aphidinea phylogeny reconstruction. Combined analyses are performed between nuclear genes and mitochondrial genes, as well as among different mitochondrial genes. New genes should be explored, and “standard markers” need to be found in aphids. The prospects of molecular systematics in Aphidinea in the future are also discussed.