Sorghum aphids (Melanaphis sorghi Theobald), are reported on a variety of host plants, from sorghum to Johnson grass to miscanthus and other grasses. This invasive insect was first reported as a pest of sorghum in 2015. We now know that the original pest outbreak was due to an introduction event. While it is established that the invasive sorghum aphid (Melanaphis sorghi) is a different species from the sugarcane aphid (Melanaphis sacchari), little is known about the potential genetic differentiation among sorghum aphids in different locations. We investigated whether aphids collected from different host plants in different parts of this aphid’s host range (Texas, Louisiana, Florida, Mexico, South Africa, and East Africa) were genetically differentiated from one another. Sequence filtering and data analysis revealed that aphids are genetically differentiated based upon collection location. Additionally, genetic differences among aphids were associated with host plant. The findings from our research can be used to inform management techniques for agroecosystems.