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<i>Pythium ultimum</i> causes seedling damping-off, and root and crown rot in greenhouse ornamental plants.  To understand the population dynamics and structure of <i>P. ultimum </i>in Michigan floriculture crops, simple sequence repeats (SSRs) were developed using <i>P. ultimum </i>transcriptome.  After screening in-silico SSR markers, six SSRs were selected based on their polymorphism after evaluation with bulk-segregant analysis of pool of <i>P. ultimum </i>isolates.  A total of 166 isolates sampled from 2011 to 2013 from greenhouses in Kalamazoo, Kent and Wayne counties were analyzed using six fluorescent-labeled SSRs.  The average genotypic diversity (0.938), evenness (0.56), and the recovery of 12 major clones, out of the 64 multilocus genotypes obtained, may suggest that <i>P. ultimum</i> is not a recent introduction into Michigan greenhouses.   Analysis revealed a clonal population, with limited differentiation among seasons, hosts and counties sampled.  Despite of the sampling effort, sample size was limited for some locations; therefore monitoring program using the markers developed in this study will help to understand further the dynamics of this population.   Results also indicate that sanitation could be enhanced in order to more completely eradicate resident <i>P. ultimum</i> populations. Finally, the presence of common genotypes among counties suggest that there is an exchange of infected plant material among greenhouses, or that there is a common source of inoculum coming to the region.