Fall armyworm, Spodoptera frugiperda (J. E. Smith), is an important agricultural pest native to the Americas that has recently been introduced into the Eastern Hemisphere where it has spread rapidly through most of Africa and much of Asia. The long-term economic consequences of this invasion will depend on how the species and important subpopulations become distributed upon reaching equilibrium, which is expected to be influenced by a number of factors including climate, geography, agricultural practices, and seasonal winds, among others. Much of our understanding of fall armyworm movements have come from mapping genetically defined subpopulations in the Western Hemisphere, particularly in North America where annual long-distance migrations of thousands of kilometers have been documented and modeled. In contrast, fall armyworm mapping in much of the rest of the hemisphere is relatively incomplete, with the northern portion of South America particularly lacking despite its potential importance for understanding fall armyworm migration patterns. Here we describe the first genetic description of fall armyworm infesting corn in Ecuador, which lies near a likely migration conduit based on the location of regional trade winds. The results were compared with populations from corn habitats in select locations in the Caribbean and South America to investigate the possible migratory relationship between these populations and was further assessed with respect to prevailing wind patterns and the distribution of locations with climate favorable for fall armyworm population establishment and growth.