An aggressive, non-native haplotype (distinct genetic lineage within a species) of Phragmites australis is invading brackish and freshwater systems in the eastern United States, potentially displacing native haplotypes. We studied the differential susceptibility of native and non-native populations collected from sites throughout North America to the non-native aphid, Hyalopterus pruni. In a greenhouse study, we found significantly higher aphid populations on native haplotypes than on the non-native haplotype 2 mo after infestation. Aphid feeding caused chlorosis and death of native stems, and in some cases, killed whole native genets. The non-native plants remained relatively undamaged. In a field study, non-native plants had significantly lower aphid densities than native plants or remained aphid free. There was an interactive effect in which aphid populations increased on the native plants over the 1-mo study period but remained low on non-native plants over the same period. The susceptibility of native North American populations of P. australis to non-native aphid infestation may indirectly affect the ability of these native plants to compete with non-native plant populations, ultimately contributing to the decline of native haplotypes.