Insect herbivore evolution is tightly linked to changes in their host plants. Many plants have defensive traits that enable them to naturally tolerate and/or deter insect herbivory (host plant resistance
HPR). Some insects have adapted to overcome or resist these defenses (virulence). Global climate change may exacerbate insect virulence, although these interactions have not been closely examined. We tested how one abiotic stressor, flooding, affects interactions between soybeans and two different biotypes of the invasive, soybean aphid (Aphis glycines). In laboratory assays, flooding suppressed avirulent aphid population growth but had no impact on virulent conspecifics, indicating a differential fitness response between biotypes. We also used RNA sequencing to compare flooding stress impacts on gene expression in virulent and avirulent aphids. There were strong, constitutive differences between biotypes regardless of flooding stress, with virulent aphids upregulating putative effector genes and differentially expressing genes involved in epigenetic regulatory processes. Within each biotype, transcriptomic changes due to flooding were limited, but overall, fewer genes were differentially expressed in virulent aphids in response to stress treatments. Our data suggested that virulence adaptations in soybean aphids may also confer greater resiliency to abiotic stress, which could accelerate selection for virulence as climate change effects intensify.