Spodoptera frugiperda (J. E. Smith) (Lepidoptera: Noctuidae) is a Neotropical species found from Argentina to the United States of America. In its distribution area, two genetically distinct strains are found that differ in their plant host distribution. The strains are morphologically identical, and they can only be reliably distinguished by molecular markers. In this study, we characterized caterpillars collected in corn, Zea mays L., and rice, Oryza sativa L., plantations in the state of Rio Grande do Sul, Brazil. The mitochondrial haplotype typical of the rice strain was found in 100% of the caterpillars collected from that crop, whereas 83% of the caterpillars obtained from corn were of the corn strain haplotype. A sex-linked tandem repeat element called FR was previously shown to have a strain-biased distribution in North American populations. We demonstrated that the same element is found in Brazilian fall armyworm and that it also organized in large tandem repeat clusters that are most frequently observed in caterpillars collected from rice and that display the rice strain mitochondrial haplotype. These results indicate that the Brazilian and North American fall armyworm populations are virtually indistinguishable with respect to the known genetic markers that are diagnostic of strain identity. Furthermore the data are consistent with other studies suggesting substantial gene flow between these widely separated populations. The strain-biased distribution of the FR element makes it a potentially useful marker to estimate interstrain hybridization frequencies of this species in Brazil.