The park is part of the Annamites eco-region. According to the results of initial surveys, the primary tropical forest in Phong Nha - Ke Bang 140 families, 427 genera, and 751 species of vascular plants, of which 36 species are endangered and listed in the Vietnam Red Book. The forest is also home to 98 families, 256 genera and 381 species of vertebrates. Sixty-six animal species are listed in the Vietnam Red Book and 23 other species in the World Red Book.
In 2005, a new species of gecko was discovered here by a group of Vietnamese biologists together with biologists working for the park, Cologne Zoo in Germany and the Saint Petersburg Wild Zoology Institute in Russia.