The Elan Estate is nationally important for its variety of lower plants (mosses, liverworts, lichens, ferns and fungi). Its semi-natural ancient woodlands are some of the finest in Britain and all are included in Sites of Special Scientific Interest. The upland bogs and mires are also very important for wildlife. Twenty-six species of sedge have been found, 11 species of rush and no fewer than 18 different bog mosses (Sphagnum spp.)

There are several species-rich hay meadows on the Estate of a type unique to parts of upland Wales. There are fewer than 100 of them left in total. On the Elan Estate the hay meadows are carefully managed to protect the great variety of wild flowers which include the rare Upright Vetch, Globeflower, Greater Butterfly Orchid and Fragrant Orchid, and two strange ferns, the Adders Tongue Fern and Moonwort.

In total 26 species of fern have been found including the Royal Fern, Beech Fern, Oak fern, Brittle Bladder Fern and the very small Wilson's Filmy Fern. Sixteen different broadleaved trees grow including the rare English Whitebeam on the cliffs above the Visitor Centre. More than 300 species of flowering plant have been found. A similar number of lichens and the same again for mosses and liverworts combined.

Seven species of orchid grow here; Lesser Twayblade, Fragrant Orchid, Early Marsh Orchid, Common Spotted Orchid, Heath Spotted Orchid, Lesser and Greater Butterfly Orchid.

Thirty-five different species of grass have been identified.