The Flora
The Sanctuary has diverse vegetation types. These are the West-coast Tropical Evergreen, West-coast Semi evergreen, Southern Moist Mixed Deciduous, Southern Hill-top Evergreen forests, Grasslands, and Marshy grasslands (Vayals). The variety of vegetation types harbours more than 680 species of flowering plants including 226 species endemic to southern Western Ghats (about 30%). Sixty nine species of plants are placed under various threat categories.

Viable populations of tree species like Meteoromyrtus wynaadensis, Syzygium stocksii, Eugenia argentea (previously considered extinct), Syzygium floccosum, Atuna indica (previously considered extinct), Coffea crassifolia (previously considered extinct), Garcinia malabarica, Humboldtia brunonis var. rakthapushpa. Atuna indica, Eugenia argentea and Humboldtia brunonis var. rakthapushpa occur only in this sanctuary.

More than 200 species of medicinal plants are reported in this sanctuary. Fifty two species of bryophytes including 28 liverworts and 24 mosses are reported. Sixteen of these are new to Kerala and 9 new to Peninsular India. Several of them are reported to occur only in this Sanctuary area. Fifty ferns reported from the area include three tree ferns.


Endemism
The high percentage of endemism in Kakkayam forest is very much comparable to other Protected Areas in South India. Actually, the percentage of endemism is higher at Kakkayam. If only tree species are considered, the percentage of endemism is far higher. There are 69 species of plants here, which are considered under various threat categories. Some trees like Meteromyrtus wayanadensis, Syzygium stocksii, Parinarium indicum, Coffea crassifolia (previously considered as extinct), Garcinia malabarica are found here with good and viable population. There are 39 species of grasses, 22 species of orchids and 28 species of legumes recognized from Kakkayam. The high representation of Lauraceae (16 species), Myrtaceae (11 species), Clusiaceae (10 species) and Melastomataceae (9 species) indicates the virginity and primary nature of this hill forest. These tree families with high percentage of endemism (up to 99% in some families) indicate the conservation significance of the area.


Bryphytes, liverworts and mosses
The area is rich in bryophytes (52 species) including 28 liverworts and 24 species of mosses (Nair et al., 2008). Several species of mosses are restricted to Kakkayam only and several others are very rare. Among these, nine species viz.,Chiloscyphus polyanthus (L.) Corda ., Cheilolejeunea subopaca (Mitt.) Mizut., Lejeunea punctiformis Taylor, Lejeunea stevensiana (Steph.) Mizut. Lejeunea subacuta Mitt., Fissidens jungermannioides Griff., Pogonatum decolyi Gangulee, Leucoloma taylori (Schwaegr.) Mitt. and Wijkia surcularis (Mitt.) H.A.Crum are new records to Peninsular India. Seven species viz., Calypogeia tosana (Steph.) Steph., Cheilolejeunea birmensis (Steph.) Mizut.,Frullania gaudichaudii Nees. & Mont., Pallavicinia ambigua (Mitt.) Steph., Bryum alpinum Huds. ex With., Diphyscium involutum Mitt. and Barbella cubensis (Mitt.) Broth. are new records to Kerala State. A preliminary study on pteridopytes brought out a list of about 52 species (Rajesh et al.)
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