Hormone-dependent responses in host plants induced by herbivore infestation have species-specific effects. This study focused on determining the relative expression profiles of the genes associated with hormone-dependent pathways in two near-isogenic wheat lines when attacked by cereal aphids. Infestation with Rhopalosiphum padi Linnaeus (Hemiptera: Aphididae) and/or Sitobion avenae Fabricius (Hemiptera: Aphididae) significantly upregulated the expression of marker genes related to the salicylic acid (SA)- and jasmonic acid (JA)-dependent pathways in the tested lines. In the resistant line 35-E4, previous infestation with R. padi significantly increased the relative expression of plant pathogenesis-related protein 1 at all sampling times but did not have a significant effect on the expression of the phenylalanine ammonia-lyase (PAL) gene. In addition, the expression levels of the lipoxygenase (LOX) and allene oxide synthase (AOS) genes immediately increased after the aphid attack. In susceptible line 35-A20, infestation with either R. padi or S. avenae led to significantly increased expression levels of the AOS and PAL genes. Moreover, sequential aphid infestation induced higher expression of AOS compared with a single-species aphid infestation, whereas the expression of the PAL gene was antagonistically affected by sequential aphid infestation. Overall, these results showed that aphid infestation induced SA- and JA-dependent responses in host plants. However, the expression profiles of these genes in resistant and susceptible host lines were significantly different.