Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae), or fall armyworm, is an important agricultural pest of several crops in the Western Hemisphere, including cotton (Gossypium L.). Two morphologically identical host strains of fall armyworm exist that differ in plant host use and habitat distribution. The corn-strain is a primary pest of corn, Zea mays L., whereas the rice-strain is the majority population infesting rice (Oryza spp.) and turfgrass (Cynodon spp.). With the increased use of Bacillus thuringiensis (Bt) toxin-expressing cotton varieties and the necessity of ensuring adequate refuge areas to prevent the spread of Bt toxin resistance, it is crucial to identify the alternative plant hosts available for the fall armyworm population infesting cotton. Stable isotope analysis combined with the molecular analysis of strain-specific markers was used to investigate whether one or both strains routinely develop on cotton grown in the Mississippi delta. We found that the majority of fall armyworm adults present during the early cotton growing season arose from C4 plants (e.g., corn and sorghum, Sorghum vulgare Pers.) and that the only strain likely to be developing on cotton (a C3 plant) in substantial numbers was the corn-strain. The population distribution patterns observed were consistent with corn providing an important refuge for the fall armyworm strain infesting cotton and suggested that late season populations in the Mississippi delta may be migrants from more northern corn areas.