Peronospora tabacina Skalický [D.B. Adam], an obligate oomycete causing blue mold of tobacco, is an important pathogen causing significant economic losses. The pathogen rarely reproduces sexually, and the windblown asexual sporangia from infected plants are the source of yearly natural epidemics. A collection of 110 isolates of P. tabacina with subgroups from across Europe, the Middle East, and the Americas was analyzed with nine genomic microsatellites to investigate population structure and pathogen diversity. Clone-corrected data revealed the presence of 34 alleles or 3 to 5 alleles per locus. Genetic variation among the 10 subgroups accounted for 7% of total variation indicating low levels of genetic differentiation and high gene flow among them. The Mantel test showed significant correlation between geographic and genetic distances (r = 0.25; P < 0.001). Evidence of linkage disequilibrium (P < 0.001) showed that several tested subgroups were partially clonal in character, whereas the markers used were distributed across the whole genome, without significant linkage disequilibrium among them (P < 0.001). Low genetic variation and lack of population structure among the analyzed isolates was attributed to continuous gene flow across continents via infected plant exchange and/or long distance dispersal of sporangia. Bayesian inference provided insights into pathogen history and origin based on several possible scenarios when linked to the host plant.