Technical Abstract: Soybean rust (SBR) is a destructive disease worldwide and is a newly emerged threat to soybean production in the United States. Although deployment of resistant germplasm is the most preferred means of disease control, there is limited knowledge about the population structure of Phakopsora pachyrhizi isolates in the US. To address this issue, a survey was conducted to define the genetic diversity and possible origins of US isolates. At least five distinct isolate types within the US were identified and most States contained a mixture of isolates. Gauged by sequences from international and archival isolates, we identified two groups of global isolates that are endemic to all continents, reinforcing the hypothesis of a global migration of P. pachyrhizi. However, we also identified a few groups that appeared to be present only in Asia, Australia, and North America, suggesting the presence of a possible alternative migratory pathway. Interestingly, one isolate type appears to be unique to the United States, suggesting either a unique origin or very rapid diversification of isolates in North America. The data provide the most comprehensive analysis to date of the genetic diversity of P. pachyrhizi isolates in North America.