Technical Abstract: Switchgrass is a promising bioenergy crop native to North America. Population genetic diversity was characterized in 12 cultivars that included upland and lowland ecotypes encompassing variation in ploidy levels, geographical origins, and breeding history using 21 EST-SSR marker loci that showed single-locus disomic segregation in tetraploids and apparently tetrasomic inheritance in octoploids. Genetic diversity was found to be greater in octoploids than tetraploids and cultivar relationships suggest an autopolyploid origin of octoploids within upland tetraploids. Model-based Bayesian clustering of individuals indicated that closely related octoploid cultivars are difficult to descriminate, possibly due to slowed differentiation by polysomic inheritance. One tetraploid cultivar displayed comparable diversity to the least diverse octoploid cultivars, suggesting breeding history or population history in the native stands of origin also affected within-cultivar diversity. Pleistocene climate oscillations may be a factor shaping the population genetic structure in the native stands and consequently the cultivars, based on the geographical distribution of genetic diversity detected. Overall and pairwise FST indicated significant cultivar differentiation. The analysis of the sampling effect indicated addition of loci and/or individuals to achieve identification in some octoploid cultivars with high accuracy appears impractical.