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<i>Fusarium virguliforme</i> is a destructive plant pathogen responsible for soybean sudden death syndrome (SDS), which results in severe yield loss of soybean. SDS was first reported in Arkansas in the 1970s, since then it has been reported in surrounding states. In South America, SDS was first discovered in Argentina and Brazil in the early 1990s and subsequently in other South American countries. In recent years, <i>F. virguliforme </i>has been detected in South Africa and Malaysia; however, little is known about the migration history of this pathogen. In this study, we conducted a population genetic analysis to demonstrate the genetic diversity and population structure of <i>F. virguliforme</i> isolates collected from multiple sites in the US and Argentina using microsatellite markers. Principal component analysis demonstrated that <i>F. virguliforme </i>isolates from Argentina clustered distinctly from the U.S. <i>F. virguliforme </i>isolates, with the exception of the Arkansas population, which overlapped with both Argentina and U.S. isolates. In a structure analysis, there was a clear distinction of population structure composition between Argentina and U.S. <i>F. virguliforme </i>populations, aside from the Arkansas population, which comprised both genotypes present in Argentina and US populations. In addition, the genetic diversity indices of the Arkansas populations were higher than the rest of the populations. These results suggest migration of <i>F. virguliforme </i>between continents.