The study of the rare plant species in technogenically disturbed habitats is a significant prerequisite to preserve their natural populations. Structural and functional characteristics of photosynthetic apparatus and biomass allocation in regionally rare orchid Epipactis atrorubens (Hoffm.) Besser (dark-red helleborine), colonizing two serpentine dumps post-asbestos mining (Anatol’sko-Shilovsky deposit, Sverdlovsk region, Russian), in comparison with the natural forest community were studied. Despite the adverse edaphic conditions (the high stoniness, excess some metals, low content of nutrients, water deficiency), quite numerous populations of E. atrorubens were found in transformed sites. The orchid plants colonizing the serpentine dumps were distinguished by the thicker leaf blade (by 23%), higher leaf mass per area and leaf density (by 36 and 12%, respectively), as well as reduced diffusion resistance to CO2 (by 30%) in comparison with plants in the natural forest community. In addition, the number of cells and chloroplasts per unit leaf area of orchid leaves had increased (by 22% on average). Though orchids grew on serpentine dumps in the unfavorable conditions, the CO2 uptake per unit leaf area and chlorophyll content decreased significantly (by 16 and 40%, respectively) only on one of the dumps, which was characterized by greater stoniness, excess light and water deficiency due to the lack of crown closure. The total fresh and dry biomass of orchid individuals from dumps was slightly less (14% on average) than that in the forest natural community. The underground biomass decreased significantly (26% on average), and at the same time aboveground biomass was higher for plant on dumps. The changes in leaf mesostructure, as well as the maintaining of photosynthetic activity contributed to stability of orchid populations in disturbed habitats. Analysis of the structural adaptations of E. atrorubens indicates that it possess a secondary ecological strategy (competitor–stress-tolerator–ruderal). Thus, the study suggests that plasticity of E. atrorubens photosynthetic apparatus promotes its successful survival in adverse environmental conditions of transformed ecosystems.