Technical Abstract: Brown stem rot (BSR), caused by Phialophora gregata f. sp. sojae, is an important yield-limiting disease of soybean (Glycine max) in the Midwestern USA. Midwestern populations of P. gregata are separated into two genotypes, A and B, based on intergenic spacer sequences of ribosomal DNA. Genotype A causes both leaf and stem symptoms, and genotype B typically causes internal stem symptoms only. Data is limited on the geographic distribution of genotypes A and B. Furthermore, data is limited on whether soybean genotypes are colonized by each pathogen genotype at different frequencies. Field plots were established at five sites in Illinois, three sites in Wisconsin, and two sites in Minnesota in two different years. Soybean cvs., Bell, BSR101, Dwight, Sturdy, Williams 82, LN92-12033, and LN92-12054 were sown with two to four replications at each field site. Stems (N = 5-10) were harvested arbitrarily per plot at the R8 growth stage and assayed by PCR to detect the A and B genotypes. Both pathogen genotypes were detected at all locations except Urbana where only genotype A detected and St. Paul where only B was detected. Genotype A was the predominant genotype detected in susceptible cultivars Williams 82, and LN92-12054, with 70 and 78% of infected stems positive for A, respectively. The other susceptible cultivar, Sturdy, mainly yielded genotype A at the Illinois and Wisconsin locations where both pathogen genotypes are present, but mainly yielded B at the Minnesota locations where genotype A was absent or undetectable. Genotype B was the predominant type detected in partially resistant cultivars BSR101, LN92-12033 and Bell, with 55, 89 and 99% of the infected stems testing positive for B, respectively. Genotypes A and B were detected approximately equally in Dwight.