Pythium ultimum causes seedling damping-off and root and crown rot in greenhouse ornamental plants. To understand the population dynamics and assess population structure of P. ultimum in Michigan floriculture crops, simple sequence repeats (SSRs) were developed using the previously published P. ultimum predicted transcriptome. A total of 166 isolates sampled from 2011 to 2013 from five, one, and three greenhouses in Kalamazoo, Kent, and Wayne Counties, respectively, were analyzed using six polymorphic and fluorescently labeled SSR markers. The average unbiased Simpson's index (λu, 0.95), evenness (E5, 0.56), and recovery of 12 major clones out of the 65 multilocus genotypes obtained, suggests that P. ultimum is not a recent introduction into Michigan greenhouses. Analyses revealed a clonal population, with limited differentiation among seasons, hosts, and counties sampled. Results also indicated the presence of common genotypes among years, suggesting that sanitation measures should be enhanced to eradicate resident P. ultimum populations. Finally, the presence of common genotypes among counties suggests that there is an exchange of infected plant material among greenhouse facilities, or that there is a common source of inoculum coming to the region. Continued monitoring of pathogen populations will enhance our understanding of population dynamics of P. ultimum in Michigan and facilitate improvement of control strategies.