Fall armyworm, Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae), is a major economic pest throughout the Western Hemisphere. There exist two morphologically identical but genetically distinct strains (corn-strain and rice-strain) that differ in their host plant preferences. These strains can be distinguished by polymorphisms in the mitochondrial cytochrome oxidase I gene. There is also a tandem-repeat genetic element called FR that is found in large sex-linked clusters primarily in the rice strain, as characterized by sampling of fall armyworm populations in the southeastern United States. It was recently shown that the FR element is also present in Brazil, where it exhibits a similar strain-biased distribution. In this article, the analysis of FR was extended to populations in southern Texas, one of the principle overwintering locations for fall armyworm that infests the continental United States. DNA sequence analysis and an optimized polymerase chain reaction (PCR)-based method demonstrated that FR sequences are present in Texas and show the same distribution pattern as observed in Florida. The distribution of FR in Florida has remained relatively unchanged over a 4-yr period, suggestive of polymorphic equilibrium and the existence of at least partial barriers to the generation of interstrain hybrids. The implications of these findings on our understanding of interstrain mating behavior and the utility of the modified detection method to study fall armyworm populations are discussed.