Soybean and corn are the major crops in the North Central U.S. Rhizoctonia zeae was recently identified as a causal agent of seedling diseases of these crops in Nebraska. Fungicide seed treatments are commonly used to manage seedling diseases and include several modes of action, such as DMI, Phenylpyrroles, SDHI, and QoI. To establish the current control level and devise better control strategies, we examined the fungicide sensitivity and population structure of R. zeae. Effective concentration for 50% inhibition (EC₅₀) was estimated for 65 R. zeae isolates to four fungicides using serial dilution. Average EC₅₀ for prothioconazole (DMI) was 0.173 ppm, fludioxonil (Phenylpyrroles) was 0.096 ppm, sedaxane (SDHI) was 0.066 ppm, and azoxystrobin (QoI) was > 100 ppm. To validate insensitivity to azoxystrobin, in planta assays will be performed. EC₅₀ did not differ significantly among isolates collected from different years (2015-2017) or crops for all fungicides (P > 0.05). A discriminatory concentration will be selected for each fungicide and EC₅₀ of additional isolates will be estimated. Results will establish fungicide sensitivity of R. zeae and can be used to monitor sensitivity shifts in future. We sequenced five R. zeae isolates at >100X coverage and identified 1,593 candidate microsatellite markers to characterize its population structure. This will allow inference of the evolutionary potential, mating system, and dispersal mechanism in R. zeae populations. Collectively, this information will help to devise better control strategies for R. zeae in the North Central U.S.