Employees of the Forest Research Institute (FRI) KarRC RAS have contributed greatly to the study of the biodiversity of vascular plants, aphyllophoroid, sac and basidial fungi and lichens of the Republic of Karelia. Studies of vascular plants and various groups of fungi have been carried out since the FRI foundation in 1957 and are continuing successfully at present, with new tasks being set and the geographic range of interests expanding to cover the entire Northwest Russia. The lichenofloristic research component appeared at FRI later (in 1985) and is also developing. Prominent scientists such as V. I. Krutov, M. L. Ramenskaya, and V. I. Shubin, Doctors of Biological Sciences who worked at the FRI, made a huge contribution to the study of the biodiversity of Karelia, Eastern Fennoscandia, and the forest zone of European Russia as a whole. The role of these scientists and their students or successors is great not only in advancing the knowledge of the species diversity of Karelia and adjacent regions, but also in treating various issues of nature protection and sustainable use of natural resources, especially forest resources. The Institute’s employees have played a leading role in building the system of protected areas (PAs) in Karelia, especially considering that the republic’s first PA, Kivach Strict Nature Reserve, used to be a FRI unit for quite long. Botanists and mycologists from FRI participated in compiling the inventory of the flora and mycobiota and in preparing scientific substantiation papers for many planned PAs. Research continues in the PAs after their designation. Employees of the FRI prepared the first (unofficial) edition of the regional Red Data Book and then participated as leading authors in the preparation of three official editions of the Red Data Book. At present, many direct students (postgraduates) or successors of the pioneers in the study of the species diversity of vascular plants and fungi V. I. Krutov, M. L. Ramenskaya, and V. I. Shubin continue to work productively at the Institute.