The rich and diverse world of plants of the Žemaitija National Park counts 811 species of plants, 214 species of mosses (69 species of plants are listed in the Red book of Lithuania as rare or endangered). There are also some species of plants that are under protection in the European Union: Botrychium simplex, Liparis loeselii, Hamatocaulis vernicosus. Some species like Cladium mariscus, Trichophorum cespitosum, Carex magellanica, Lunaria rediviva, Salix lapponum, Primula farinosa are relicts of glacial times.
Biologists are amazed by numerous populations of Platanthera chlorantha, Pinguicula vulgaris, Dactylorhiza maculata, Dactylorhiza ochroleuca, Dactylorhiza longifolia, Liparis loeselii, Listera cordata. The only place of growing of Botrychium simplex was found here. Some of the Park's areas are geographic ranges of some species of plants: the northern part – of Mentha longifolia, northwest –of Aquilegia vulgaris, eastern – of Trichophorum cespitosum.