The majority of Motutapu is in farmed pasture. The original forest has gone but there are small post- eruption native forest remnants including puriri, karaka, taraire, tawapou, mangeao, kohekohe, and flax. Pohutukawa trees grow on the coastal fringe.

There are now approximately 100 hectares of volunteer restoration planted native forest. The island is also host to a number of unwanted plants including rhamnus (evergreen buckthorn), moth plant, woolly nightshade, apple of Sodom, pampas and smilex. These pests are being brought under control through a concerted weed programme. Some exotic trees, planted by the early European settler farmers, such as Norfolk Island pine, macrocarpa, pinus radiata and poplars can be seen in the landscape.

Originally Motutapu would have been covered with coastal lowland forest similar to that growing on Waiheke and other Hauraki Gulf islands. The Rangitoto eruption, 600 years ago, understandably had a major impact on this forest as volcanic ash covered island.  Since the arrival of Europeans in 1840 the mixed broadleaf/podocarp forest has been cleared to the point where today the island is mostly in pasture grasses with only small remnants of the post eruption forest dotted across the island and around the coastal strip.

The forest remnants include pohutukawa, tawapou, kohekohe, taraire, mahoe, puriri, kowhai, mangeao and karaka.  Most of the native vegetation that is growing naturally occurs in the coastal fringe (cliffs, cliff tops and dune areas) and is made up predominantly of pohutukawa some of which are quite old and very beautiful.

The island is undergoing a major transformation with volunteers from the community planting a native forest. Since 1994 approximately 100 hectares have been planted with over 500,000 eco sourced native saplings raised in the Trust’s island nursery by volunteers. The Home Bay Forest is the largest area of native trees, many now over seven metres high with dozens of native seedlings regenerating naturally under the rapidly growing canopy.

The majority of the initial trees planted are species such as manuka, kanuka, coprosma, ake ake, cabbage trees, flax, houpara (five finger), ngaio, karo, and mahoe – to help establish the forest. After these first phase plants, bigger species that will form the canopy are being planted in the habitat which has been created. These include puriri, pohutukawa, rewarewa and kowhai,  tawapou, taraire, tawa, nikau, kauri, kahikatea, kohekohe, karaka, mangeao, tanekaha and wharangi. Native ferns such as shaking brake and mamaku (black tree ferns) are introducing themselves into the native plantings.

Motutapu has not escaped the introduction of imported plants. There are a number of large exotic trees planted by the early European settler farmers. Norfolk Island pines can be seen in Home, Station and Emu Bays and there are a number of shelter belts of macrocarpa, cryptomeria, gum trees and pine trees scattered across the island. Surrounding the Reid Homestead and alongside the stream in Home Bay there is an interesting array of exotic trees including Moreton Bay and Port Jackson figs, Norfolk Island Hibiscus, walnuts, flame trees, and London planes.

The island is host to a large number of unwanted plants including rhamnus (evergreen buckthorn), moth plant, woolly nightshade, apple of Sodom, pampas and smilex. Some of these species pose a serious threat to the native plantings. There is a year-round programme of weed control by volunteers and contractors to combat these plant pests.