The study included the protected areas of Donduşeni rayon: Botanic Natural Monument(BNM) Rudi-Gavan, Natural Reservation of Medicinal Plants (NRMP) Cernoleuca, Landscape Reservation(LR) Rudi-Arionesti, representative ecosystems: forests Donduşeni and Horodişte. The researched areas are subject to transboundary pollution with SO2 and NOx from the Northwest. The content of heavy metals in the soil does not exceed the maximum admissible concentration, but there is a tendency to accumulate the Pb and Cu in the litter from NRMP Cernoleuca. Basing on the lichenoindication method was established that in the Forest Donduşeni air is weak polluted with SO2, but in the LR Rudi-Arionesti, BNM Rudi-Gavan and NRMP Cernoleuca, it is moderately polluted. Were recorded eight new habitats for five rare species and augmented the possibility of creating the Natural Forest Reservation Horodişte.