Limited information exists on molecular genetic variation and distribution of the corn and rice strains of the fall armyworm, Spodoptera frugiperda (J.E. Smith). This study was conducted to investigate the genetic structure of S. frugiperda across a part of its range in the United States. A 608-base-pair portion of the mitochondrial cytochrome oxidase I and II genes was sequenced from 71 individuals resulting in three corn and four rice strain haplotypes. Genetic divergence between the two strains ranged from 0.66 to 0.99%. A 562-base-pair region of the nuclear ITS-1 gene was also amplified and sequenced from 17 individuals representing both corn and rice strains. No variation was detected in any of the samples for the ITS-1 region. Analysis of molecular variance was conducted on the resulting mtDNA haplotypes from the Arkansas and Florida populations and as a hierarchical analysis between populations in the two states. Results indicate a significant overall Φ_ST for all populations with the hierarchical analysis revealing that this significant Φ_ST is due to structuring of the populations between states. The observed genetic structure is possibly due to the distribution of fall armyworm strains.