Greenbug (Schizaphis graminum) is one of the most important aphid pests in small grain crops including wheat (Triticum aestivum L.) in the southern Great Plains of the US. Wheat breeding program at Texas A&M University has introgressed several greenbug resistance genes into released cultivars, including TAM 110 and TAM 112, however the molecular mechanisms of the resistance remain unknown. A microarray study was conducted to evaluate the transcriptomic differences in the near isogenic resistant (TXGBE273) and susceptible (TXGBE281) wheat lines using Affymetrix GeneChip wheat genome array with 55K transcripts. The leaf samples were collected from greenhouse grown bulked resistant and susceptible wheat lines at 0, 24, and 48 hours after infestation. The microarray data analysis suggests that within 24 hours after greenbug feeding the genes related hormone and amino acid biosynthesis, metabolism, cell wall modification, defense signaling, secondary metabolites, etc. were differentially regulated between the resistant and susceptible lines. Overall, these results offer numerous opportunities to understand the molecular basis of resistance mechanisms to greenbug feeding and help in developing wheat cultivars with better resistance.