We compared the morphology, physiology, and stem-count change of natural versus transplanted endangered orchids (Cypripedium japonicum) undergoing habitat management (repeated removal of competing understory vegetation) during 2009 and 2013 in South Korea. The restored site had lower transmitted light and soil humidity than the natural site. The natural and restored populations differed in leaf morphology and chlorophyll content (natural: total chlorophyll = 1.00 ± 0.04, restored: total chlorophyll = 0.53 ± 0.06). No recruitment occurred during the monitoring period. Population viability tended to decrease in the restored population (λG=0.97,μ=– 0.05, σ2=0.036) and increase in the natural population (λG=1.07,μ = 0.03, σ2=0.075). In conclusion, restored C. japonicum have poor long-term viability compared with plants in the natural habitat, a difference caused mainly by inappropriate transplant-site selection. Repeated removal of competing vegetation differed in its effects on character, abundance, and reproductive properties in both populations. Notably, habitat management increased stem count and flowering rate in natural C. japonicum, but these changes did not cause an increase in fruit-setting rate.