Though the Ceram flora is poor in species diversity in comparison with the neighbouring islands, as well as Sulawesi (Celebes) and Irian Jaya (West Papua), but phytogeographically it is important, because Ceram and the adjoining island functionally forms a land bridge for the transition zone between West and East Malesian flora, for an example, in Manusela National Park can be found at least three genera of the Dipterocarps a family which dominates the West Malaesian region.

The northern lowland alluvial plains comprise a diversity of vegetation types such as the mangrove, fresh-water swamp forest, the dry land and the hill mixture Dipterocarp-Agathis forest, and along the river banks, the Eucalyptus trees, form a quasi pure stands, and it gives an impressive scenery with a canopy to 50 m high.

The sub montane and montane vegetations, occupies almost one third of the park area (manusela, Merkele and Kobipoto ridges). Here can be found the Damar forest (Agathis alba) and grows in association with meranti (Shorea sp.), and sporadically, the dense bamboo forest and the thorny rattans make venturing off the cut paths almost impossible.

Most fascinating plantlife is the mossy or cloud forest extending upward from 1,500 m. Here gnarled, often stunted trees are covered thickly by mosses, lichens or orchids, and in this zone, the unique flower of the lady's slipper orchid usually grows on the steep limestone walls along a deep valley of the river.
The park's fauna is much less specialized than its plantlife, and is more representative of Wallacean region, as a transitional zone between Asian and Australian faunas. Typically Australian are the oriental and spotted phalanger, megapodes, cassowaries and numerous parrot species. In addition Ceram has 14 endemic birds, 6 endemic mammals, and several endemic butterflies, including the giant birdwing butterfly (Ornithoptera goliath procus) and the beautiful Delias (D. manuselensis)