Multi-locus genotypes were inferred using 4 microsatellite loci from individual above-ground shoots (ramets) of the wavyleaf thistle Cirsium undulatum to elucidate below-ground clonal structure without destructive excavation. Leaf tissues from approximately 500 ramets were collected from ten 12x12 m plots at two mixed grass prairie sites in the Sand Hills region of western Nebraska. Ramets with identical genotypes were inferred to form a single genetic individual (genet), and assumed to be connected below ground via lateral root shoots to a common taproot. Confidence of genet designations was assessed using the probability of identity, which is calculated with allele frequencies from each site. X-y coordinates taken after tissue collection were used in mapping genets to visualize their spatial spread, and to estimate pair-wise distances among ramets of each genet. The average number of ramets per genet, along with metrics of clonal spread (average and maximum distance between all ramets of a genet), were calculated to characterize clonal structure. These metrics were used to assess the effect of land use (e.g. grazing or mowing) on the life history of C. undulatum. Most plots consist of many genets with few ramets, and few genets with many ramets. Microsatellite genotypes provide insight into the affect of land management regime on the below ground clonal structure of genets at both sites. The results of this study will be integrated into data from a long term demographic study to better understand the role of clonal propagation in survival and fecundity in facultatively clonal plant population dynamics.