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Gut microbiomes profoundly influence insect health and mediate interactions between plant hosts and their environments. Insects, including aphids, harbour diverse obligate symbionts that synthesize essential nutrients and facultative symbionts that enhance host fitness in specific ecological contexts. Sorghum (Sorghum bicolor) is a significant cereal crop cultivated worldwide that has been negatively affected by the presence of an invasive piercing-sucking insect pest, the sugarcane aphid (SCA; Melanaphis sacchari). We previously identified SC265 and SC1345 as the resistant and susceptible sorghum lines, respectively, among the founder nested association mapping (NAM) population. Here, using these resistant and susceptible lines, we explored variations in the SCA gut microbiome when they feed on two different sorghum lines with varied resistance levels. Analyses after excluding the obligate endosymbiont Buchnera aphidicola from the dataset showed a significant difference in microbial diversity and composition between resistant and susceptible sorghum lines 7- and 14 days post aphid infestation. Our results indicate that the SCA fed on susceptible and resistant sorghum lines had Pseudomonadaceae and Rhizobiaceae, respectively, as the most abundant bacterial families. Differences in gut microbial community composition were underscored by alpha diversity metrics and beta diversity compositional analyses. These findings contribute to our understanding of the intricate interplay between plant and aphid microbiomes, shedding light on potential avenues to bolster sorghum resistance to SCA.