In aphids, an identification system based on adult morphology is difficult to apply to larvae or adults of a different morph because of their small size and extensive polymorphism. In this work, identification of aphids using random amplified polymorphic DNA (RAPD) fingerprinting to generate species-specific primers was studied. A total of 20 RAPD primers were screened on eleven members of Aphidinae, i.e., Acyrthosiphon pisum, Aphis craccivora, Aphis gossypii, Aphis rumicis, Cavariella salicicola, Indomegoura indica, Lipaphis erysimi, Myzus formosanus, Myzus hemerocallis, Myzus persicae, and Toxoptera odinae. DNA fragments potentially useful as species-specific markers were selected for six aphid species. A primers set, A02ApF/A02ApR, based on the nucleotide sequence of a specific 462 bp fragment obtained from Ac. pisum by RAPD-PCR using primer A02, amplified this fragment only from Ac. pisum genomic DNA, but not from that of other species. The specificity of the primers for M. persicae was further confirmed using individuals from several field populations. It is concluded that RAPD PCR-SCAR (sequence characterized amplified region) DNA assay is a useful method for the detection of species-specific DNA fragments in mixed populations, and that pertinent data could facilitate development of a realistic quarantine system for pea aphids.