Given the challenges posed by climate change, ecological restoration is crucial for conserving biodiversity and improving environmental resilience. Ecological restoration aims to maintain and restore plant populations with high evolutionary capacity and facilitate beneficial genotype dispersion to adapt to environmental pressures. However, genetic diversity has been overlooked in restoration research. This study evaluated the genetic diversity of Lespedeza cuneata G. Don, a species targeted for restoration on the Korean Peninsula. Lespedeza cuneata is widely distributed in the Korean Peninsula and East Asia. However, this study confirmed that the heterozygosity of L. cuneata was relatively lower than that in studies of congeneric species. Analysis of the genetic structures on the peninsula revealed four clusters distinguished between several locations, and principal component analysis also identified clustering among four groups. Analysis of molecular variance results revealed that there was greater variation among (38.09%) than within (23.75%) populations, which is potentially due to the independent genotypes found in several of the populations. This study contributes to the understanding of genetic diversity within species targeted for restoration and provides valuable insights into the formulation of effective restoration plans integrating genetic aspects.