Fall armyworm is a significant agricultural pest in the United States, affecting most notably sweet corn and turfgrass. Two morphologically identical strains, rice strain (R-strain) and corn strain (C-strain), exist that differ physiologically and behaviorally and can be identified by mitochondrial haplotyping. Recent studies of overwintering populations in Florida indicate that the mitochondrial lineage associated with the R-strain itself consists of two genetically distinct subgroups, with one having molecular markers consistent with interstrain hybridization between R-strain females and C-strain males. To test this possibility and examine the ramifications of interstrain mating on population behavior and strain fidelity, larvae and adult males were tested for genetic marker combinations representative of the host strains and potential hybrids. These studies showed a sexually dimorphic distribution pattern for a sex-linked marker that is a predicted result of interstrain mating. Despite evidence of substantial interbreeding in the overwintering sites, both FR and the strain-diagnostic mitochondrial markers still showed the plant host and habitat biases associated with the host strains, indicating that strain integrity was largely maintained. However, there is evidence that the two R-strain subpopulations differ in habitat distribution in a manner suggestive of the “hybrid” genotype being less specific in its plant host preference. The existence of a genetically distinct hybrid subpopulation must be taken into account when evaluating fall armyworm population dynamics and infestation patterns in overwintering areas.