Within Kalaupapa National Historical Park’s 10,700+ acre boundary are remnants of native plant and animal communities, and plants carried to Hawai`i by the early Polynesians. The park contains habitats ranging from the ocean to the upland rain forest. Nearly 20 federally-listed threatened and endangered species of plants and animals have been identified within the park.

The park’s boundary extends for a quarter mile offshore and includes 2,000 acres of ocean, two small islands and wet shorelines. All support a wealth of fish and wildlife resources. On the small islands of `Okala and Huelo are found loulu palms, the only native genus of palms, and the endemic pua`ala, which can be found only on the sea cliffs and off shore islands of Moloka`i from Kalaupapa east to Halawa.

The coastal spray zone, located along the northeast shore of the peninsula, contains predominantly native plant communities. This habitat contains several federally endangered plants including the endemic haha, and alani. The endangered Carter's Panic grass can be found on the Kuka`iwa`a Peninsula. Native Hawaiian vegetation in the coastal spray zone includes `illima, hinahina, and naupaka.

The threatened Tetramolopium rockii is found only in northwest Moloka`i.

Native vegetation can also be found within Kauhako Crater. Endemic `ohe makai and wiliwili forest in the crater is the only remaining windward coast community of its type, low elevation dryland forest, known in the state of Hawai`i. 

A lake at the bottom of the crater, less than one acre in surface area, is more than 800 feet deep and contains a sub-species of shrimp, which may be unique to this lake.

Twenty known lava tubes and caves on the peninsula contain endemic invertebrate species and as yet incompletely inventoried flora and fauna. The Kauhako Trench, a collapsed lava tube about one mile in length and running north from Kauhako Crater, contains vegetation established in an environment protected from wind and ocean spray as well as browsing and trampling by deer, pigs, horses, and at one time, cattle.

Na pali, or sea cliffs, rising thousands of feet above the peninsula and ocean, separate the peninsula from the rest of the island of Moloka`i. Native vegetation such as `awikiwiki, and makou survives here because of the relative inaccessibility. Hala trees are native to Hawai`i and can grow from the shorelines to 1,000 foot elevation on the cliffs. This area has been designated as the North Shore Cliffs National Natural Landmark (1972), recognized as a significant remaining example of sea cliffs in the nation’s natural heritage.

Waikolu Valley contains the park's sole perennial, or ever-flowing, stream, and one of only four such streams on the entire island of Moloka`i. The stream contains all five native diadromous (goby) fish species, native snails and shrimp. Surface and groundwater withdrawn from Waikolu is the source of most water for the entire western half of Moloka`i.

Pu`u Ali`i-`Ohi`alele Plateau, on top the cliffs to the east of Waikolu Valley, is one of the best examples of `ohi`a rain forest in Hawai`i. It provides essential habitat for rare native forest birds, including the `Amakihi, `Apapane, and the `I`iwi. In this intact native forest are varieties of ferns and peperomia.

Polynesian plant introductions can be found on the peninsula and throughout Kalaupapa settlement. Hawaiians used ti for food wrappers, thatch for houses, and sandals. The bark of wauke was beaten into fiber for kapa cloth. Bananas and coconut palms provided food, while noni provided medicine and dye.

Invasive, non-native plants are a severe problem throughout the state of Hawai`i. Within the park the predominant alien vegetation is Christmas berry, koa haole, and lantana. These aliens threaten the remaining native and endemic vegetation.

Non-native animals damage the remaining native plants and animals as well. Cattle, brought in for residents of the isolation settlement, have been removed from the peninsula but other introduced animals remain, including axis deer, feral goats, and feral pigs. Mongoose and rats are also present. None of these animals have natural predators, and all threaten what remains of Hawai`i’s natural heritage at Kalaupapa.