Aphids are among important agricultural pests. The pest's evolutionary tendency towards a loss of taxonomically useful characteristics, as well as morphological plasticity due to host type and as a result of environmental factors, make a morphological identification of aphids difficult, whereas exact identification is indispensable for managment of these pests. Thus, modern identification methods could help in managing these pests. In this study conducted during 2008-2010 on trees in pome fruit orchards in Mashhad region of Iran, classic method accompanied with DNA barcoding was employed for an identification of aphid pests. Aphis pomi, Dysaphis afiinis, D. plantaginea, Nearctaphis bakeri and Allocotaphis quaestionis were collected from apple, quince and pear trees, A. quaestionis being reported for the first time from Iran. DNA barcoding was provided for cox1 gene in these species and phylogenetic relationship investigated among the collected species as well as other species within the family. DNA barcoding confirmed the morphological identification. Results of molecular data were compatible with morphological characteristics and classic grouping, separating the studied species as based on genus and tribe. This is the first data gathered about aphid characterization in Iran while applying DNA barcoding. The results of this study indicate that cox1 sequence could be useful in aphids' identification and recognition of their internal relationships.