Ypäyssuo is the largest mire system in Karelia, which in 2015 was, together with a big part of the Kepasuo mire system, included in the newly established regional hydrological (mire) nature reserve (zakazknik) Ypäyssuo. The Ypäyssuo mire system was surveyed by different specialists in 1954, 2003 and 2010. In 2013 surveys focused on the flora of mire, forest, aquatic, waterside, secondary and disturbed habitats, including the previously understudied mires of the Kepasuo system. This paper provides up-to-date information on the flora of vascular plants and mosses in this protected area. The list of species and their occurrence in the reserve's habitats are reported for the first time. Surveys of the territory detected 242 species of vascular plants and 111 species of mosses. The diversity of the flora is not high, the greatest contribution to the biodiversity coming from riparian spruce forest and waterside habitats, which occupy less than 3 % of the reserve's territory. They harbour 128 vascular plant species (53 % of the total number) and 53 moss species (48 %). Mires, which occupy 67 % of the territory, are the habitats for 76 vascular plant species (31 %) and 51 moss species (45 %). The flora was found to comprise a number of boreo-nemoral species growing close to the northern limits of their distribution range. Dactylorhiza traunsteineri is listed in the national Red Data Book, and the Republic of Karelia Red Data Book lists also Carex laxa and Orthotrichum gymnostomum.