Yakushima Island's climate ranges from subtropical to cool temperate, which has created a rare combination of vegetation: subtropical trees near the coastline, and chinquapin and laurel dominating higher elevations. Yakusugi—cryptomeria trees over 1,000 years old—are unique to the area.
The park's forests shelter many endemic creatures, such as Yaku shika (a subspecies of the sika deer) and Yakushima zaru (a subspecies of the Japanese macaque). Yakushima Island is also an invaluable nesting ground for loggerhead turtles.
The island of Kuchinoerabujima is home to many rare creatures, including the Erabu flying fox and Erabu black-banded sea krait.