It is formed from schist, phyllite, and sandstone, and dates from the Tertiary period to the mid-Mesozoic era.

[2] Mount Yonaha is at the center of the Yanbaru forest that spans the villages of Higashi, Kunigami, and Ōgimi.

Yanbaru contains some of the last large surviving tracts of subtropical rainforest in Asia, and the mountain is lush with evergreens forests.

While Mount Yonaha is an important natural habitat to numerous species of plants, birds, and animals, its ecology has been negatively affected by agricultural development at its base, and lumbering and the subsequent establishment of second-growth forest.

[3] Mount Yonaha's summit is approximately 2 km (1 mi) west of the border of Camp Gonsalves, a jungle warfare training center of the United States Marine Corps.