The sanctuary has a fabulous wealth of flora spread in the ever green and semi-evergreen forests. An amazing 1966 species of flowering plants grow in the sanctuary. Of this about 516 are endemic to the Western Ghats. For those who love orchids, this is a paradise with around 145 species of which 53 are endemic to the region. The queen among them is a ground orchid Habenaria periyarensis, which has only been found in the Periyar woods. Taeniophyllum scaberulum, which was long thought to be extinct, has also been reported. Bulbophyllum macraei, Pecteilis gigantea and Vanda thwaitesii are other special inhabitants belonging to the orchid family.
The sanctuary is a repository of medicinal plants numbering to about 300. Some are endemic to the region like Syzygium periyarensis (a tree), Habenaria periyarensis (an orchid) and Mucuna pruriense thekkadiensis (a climber). Some other important plants are Gloriosa superba, Pterocarpus marsupium, Gymnema sylvestre and Hemidesmum indicus.