DNA barcode (mitochondrial COI) has been widely attempted for species identification of many animal groups including aphids. In this study, we newly found a DNA barcoding problem in a case study of the grain aphid, Sitobion avenae. Unexpectedly, five S. avenae individuals showed considerable differences of, on average, 32.6% in the DNA sequences from other conspecific individuals. BLAST search revealed that the five sequences are similar to those of aphid parasitoids such as Aphidius, Ephedrus, and Praon spp. (Hymenoptera: Braconidae). Based on these results, we concluded that the universal primers used in aphid DNA barcodes can amplify barcode sequences from parasitoid species within host aphids.