The fall armyworm, Spodoptera frugiperda (J. E. Smith), consists of two sympatric strains (rice and corn) that are morphologically identical. To facilitate strain identification, a polymerase chain reaction (PCR)-based method was developed to detect FR, a reportedly strain-specific element found in the nuclear genome in large tandem-repeat clusters. The efficacy and accuracy of the PCR method were tested on inbred laboratory lines of both rice and corn strains. Although it was previously thought that FR sequences were exclusive to the rice strain, we were able to isolate homologous sequences in a subset of the corn strain population. Even in these cases, the PCR method detected strain-specific amplification patterns, indicating that the distinction between rice and corn strains is caused by differences in copy number and organization in the genome rather than simply the presence or absence of FR. A second polymorphism detectable by PCR was also found that distinguishes between rice and corn strain laboratory colonies. The availability of PCR-based methods for detecting strain- and population-specific molecular markers will facilitate studies on strain distribution in the field and the examination of strain-specific behavior.