Aphis craccivora Koch (Hemiptera: Aphididae) or cowpea aphid is a polyphagous insect pest that feeds on a variety of leguminous plants. We determined the contribution of host-associated genetic differentiation on population structure using the sequence data generated from analysis of mitochondrial cytochrome b oxidase (Cytb) and nuclear elongation factor-1 alpha (EF1-alpha) of A. craccivora collected from cultivated yardlong bean [Vigna unguiculata (L.) Walp. ssp. sesquipedalis (L.) H. Ohashi.] (Fabales: Fabaceae) and winged bean [Psophocarpus tetragonolobus (L.) D.C.] (Fabales: Fabaceae). Phylogenetic and haplotype network analyses revealed no evidence of strong host plant or geographical clustering in both the mitochondrial and nuclear gene dataset. A moderate, low-magnitude genetic distance (F_ST) between host plants and geographical localities was found in this study. An analysis of molecular variance (AMOVA) revealed that host plant and geography do not influence the structure of genetic variation in A. craccivora populations. Genetic variation between host plants at a location and host plants among locations demonstrated no consistent result for population subdivision of A. craccivora. These results suggest that geographical location and host plants do not significantly influence the genetic structure of A. craccivora, and this might be due to their high reproductive (parthenogenesis) ability and high migration (airborne) between host plants and regions of the country.