Spodoptera frugiperda is an important pest throughout the Western Hemisphere, particularly in corn, cotton, rice, and sorghum, among other crops. This insect has evolved two strains named the corn and the rice strains, as they have been their most frequently used hosts. However, the corn strain can also be found in cotton and the rice strain in pasture grasses and corn. Both strains have been identified by using different molecular markers, including allozymes, polymerase chain reaction—restriction fragment-length polymorphism, amplified fragment-length polymorphism, and FR tandem repeat unit, among others. So far, all reports have claimed no morphological differences between the strains. However, none of these studies have used geometric morphometrics, as we performed in this work. We applied wing morphometrics to analyze wing size and shape in 159 individuals of the corn and the rice strains reared under laboratory conditions since 2009 and already genotyped. Our results demonstrated that wing morphometrics is a promising tool to differentiate both strains, as they were statistically significant in wing shape. We also found that this species presents sexual dimorphism in the rice strain in wing shape and that wing size differs between males of both strains. Further studies will require the use of this new tool in field populations, as their identification is relevant, given that they exhibit reproductive isolation and differences in susceptibility to chemical and biological controls, suggesting they are in the process of speciation via host plant association.