In recent decades, an increasing number of plant species have been negatively affected by anthropogenic habitat fragmentation and disturbance. In many cases, the habitat matrix between populations has been converted from a natural to an urban environment. One such species, Lilium philadelphicum (Liliaceae) a showy perennial with a naturally patchy distribution, currently has populations in parts of its range in North America that persist on highly urbanized and fragmented landscapes. In this study, we used six nuclear microsatellite loci to characterize the amount and apportionment of genetic diversity among 12 remnant populations in the Midwest United States. Genetic diversity was high (7–31 alleles per locus, mean H_O  =  0.44–0.70). An analysis of molecular variance (AMOVA) detected a low level of genetic structure (F_ST  =  0.06, P < 0.001), and no effect of isolation by distance among sites (r²  =  0.02, P  =  0.28). Principle coordinate analysis (PCoA) of inter-individual genetic distances revealed essentially no structuring with PC axes one and two explaining only 22.5 and 19.7% of the observed variation respectively. Moreover, Bayesian exploration of population structure supported this observed lack of structure with a low optimum number of estimated genetic “clusters” (e.g., populations; K  =  1). If habitat fragmentation does affect gene flow among populations we cannot yet detect a strong genetic signature of this process; most likely due to the recency of landscape disturbance relative to the long generation time of this species. These results suggest that the genetic composition of these remnant populations is relatively homogenous and as such, provides land managers with a large potential germplasm source with a broad genetic base for use in local restoration activities.