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The purpose of this research was to evaluate the genetic similarity and structure of the fall armyworm, Spodoptera frugiperda (J.E. Smith), populations associated with maize and cotton crops in Brazil using amplified fragment length polymorphisms. Mean genetic similarity among populations was 0.45. The unweighted pair group method with arithmetic mean analysis dendrograms did not separate populations of S. frugiperda into clusters related to the host plant in which the insects were collected. No genetic variation was observed among maize and cotton populations of S. frugiperda, suggesting that the same populations are injuring both crops in Brazil. This research validates the need for stewardship of crop-protection methods for managing S. frugiperda to reduce the incidence of pesticide resistance, due to the spatial and temporal overlapping of maize and cotton crops in some regions in Brazil.