The clonal, necrotrophic plant pathogen, Sclerotinia sclerotiorum is the causal agent of white mold on soybean, which causes significant losses for Brazilian farmers each year. While assessments of population structure and clonal dynamics can be beneficial for determining effective management strategies, few studies have been performed. In this paper, we present a population genetic analysis with 11 microsatellite loci of 94 isolates of S. sclerotiorum from soybean fields in six Brazilian states (Goiás, N = 18; Rio Grande do Sul, N = 16; Paraná, N = 15; Bahia, N = 13; Minas Gerais, N = 7; Mato Grosso do Sul, N = 5) with Argentina (N = 5) and the U.S. (N = 15) as outgroups. Genotyping identified 87 multilocus genotypes with 81 represented by a single isolate. The pattern of genetic diversity observed suggested populations were not strongly differentiated because despite the high genetic diversity, there were few private alleles/genotypes. In addition, no multilocus genotypes were identified in both South and North America while one multilocus genotype was shared between Argentina and Brazil. Pairwise analysis of molecular variance between populations in Brazil revealed nine out of 15 pairs significantly different (P > 0.05). The population from the U.S. was most strongly differentiated in across all measures of population differentiation. Overall, our results found evidence for gene flow across populations with a moderate amount of population structure within states in Brazil. We additionally found shared genotypes across populations in Brazil and Argentina that suggests sclerotia may be transferred across states either through seeds or shared equipment. This represents the first population genetic study of S. sclerotiorum to cover a wide geographic area in Brazil.