Gene introgression between related pest populations is an important component in the assessment of how rapidly economically important traits, such as pesticide resistance, can spread within a region. An example of this is provided by the noctuid moth Spodoptera frugiperda (J.E. Smith), or fall armyworm, which is composed of two ‘host strains’ that differ in their host plant preferences. Resistance to a Bacillus thuringiensis toxin has been observed in some populations and there is concern about its spread throughout the Western Hemisphere. If this trait is easily transmitted between strains, it would expand the range of plants affected and make control efforts more difficult. A complicating factor is that the strains are morphologically indistinguishable and can only be identified by a small number of genetic markers. As a result, little is known about the frequency of interstrain hybridization in the wild. This study uses a novel strategy involving comparisons between two single-nucleotide polymorphisms (SNPs) to quantify the frequency of interstrain mating in field populations.The results demonstrate that hybridization between strains is 4- to 5-fold reduced compared to that within strains. In addition, it appears that directional interstrain mating biases observed in laboratory studies are probably not a major factor in determining the distribution of hybrid genotypes in field populations. The differential SNP technique is a significant improvement over current methods for identifying interstrain hybrids and should facilitate our understanding of fall armyworm strain and hybrid distributions in the field and the frequency of genetic exchanges between strains.