Flora

Plants

431 different vascular plants have been found in Karula National Park. Thirty-eight of the species belong to tree and shrub layers, two of the species, namely the mezereon (daphne mezereum) and the European white alm (ulmus laevis), are under protection.
393 of the found species belong to herb layer. Thirty plants in this list are protected in Estonia, eight of them are red-listed, including the Baltic orchid (dactylorhiza baltica), flecked marsh orchid (d. cruenta), narrow-leaved marsh orchid (d. russowii), broad buckler-fern (dryopteris dilatata), fragrant orchid (gymnadenia conopsea), fen orchid (liparis loeselii), pincushion flower (scabiosa columbaria), and least water-lily (nuphar pumila). A very rare species in Estonia – the daisyleaf grape fern (botrychium matricariifolium) – grows in only three known locations and one of these is in Karula.
Rare plants are mainly threatened by intensive trampling, change in light conditions and uncontrolled gathering.
140 moss species have been found in the park, eight of these are listed in Estonian Red Data Book: the Heller's blazing star (anastrophyllum hellerianum), turpswort (geocalyx graveolens), many-leaved pocket-moss (fissidens pusillus), slender green feather-moss (hamatocaulis vernicosus), three-ranked hump-moss (meesia triquetra), feathered neckera (neckera pennata), broad-nerved hump-moss (paludella squarrosa), and swamp silk-moss (plagiothecium ruthei). Twenty-six moss species do not grow near human habitation.
Mosses are threatened by air pollution, intensive trampling, forest fires and scarcity of touchwood.

Mushrooms

Mushrooms have not been studied very thoroughly in the national park, yet some interesting and rare species have been found; for example, the stout agaric (amanita excelsa), alder agaric (a. friabilis), peppery milk cap (lactarius piperatus), weeping milk cap (l. volemus), stinking russula (russula foetens), several species of pseudohygrocybe and camarophyllus. Some species of inky caps (coprinus) and Josserand's lepiota (lepiota josserandi) are the first findings in Estonia.
Living conditions of mushrooms are threatened by the removal of dead wood from forests and damage to the ground during forest extraction.