The park is part of the Annamites eco-region. By far the largest vegetation type is tropical dense moist evergreen forest on limestone under 800 m above sea level. 96.2% of this national park is covered with forest, 92.2% of which is intact primary forest. 74.7% (1104.76 km2) of the park is covered with evergreen tropical wet forest on limestone rocks at the elevation of under 800 m; 8.5% (126 km2) is evergreen tropical wet forest on limestone rocks at an elevation higher than 800 m; 8.3% (122.2 km2) evergreen tropical wet forest on soil mounts at the elevation of under 800 m; evergreen tropical wet forest on limestone rocks at the elevation of under 800 m; 0.7% (10.7 km2) evergreen tropical wet forest on limestone rocks at the elevation of above 800; 1.1% impacted evergreen tropical wet forest on limestone rocks; 2.8% (42.12 km2) impacted evergreen tropical wet forest on soil mounts; 1.3% (1,925) grass, bush on limestone rocks; 2% (29.5 km2) grass, bush on soil mounts; permanent wetland forest: 1.8 km2; rattan and bamboo forest: 1.5 km2; and agricultural plants: 5.21 km2 or 0.3%.According to the results of initial surveys, the primary tropical forest in Phong Nha-Kẻ Bàng consists of 140 families, 427 genera, and 751 species of vascular plants, of which 36 species are endangered and listed in theVietnam's Red Data Book.
The most common tree species in this park are Hopea sp., Sumbaviopsis albicans, Garcinia fragraeoides, Burretionendron hsienmu, Chukrasia tabularis, Photinia aroboreum and Dysospyros saletti. Seedlings can only grow in holes and cracks in the limestone where soil has accumulated, so in general regeneration after disturbance is slow. The forest type in this national park is dominated by evergreen tree species with scattered deciduous trees such as Dipterocarpus kerri,Anogeissus acuminate, Pometia pinnata and Lagerstroemia calyculata. In this park, the dominant plant families are the Lauraceae, Fagacaeae, Theaceae and Rosaceae, with some scattered gymnospermssuch as Podocarpus imbricatus, Podocarpus neriifolius, and Nageia fleuryi.
In the park is a 50 km2 forest of Calocedrus macrolepis on limestone (Calocedrus rupestris) mounts with about 2,500 trees, 60,000 per km2. This is the largest forest with this tree in Vietnam. Most of the trees here are 500–600 years old. These trees are listed in group 2A (rare, precious and limited exploitation) of the official letter 3399/VPCP-NN dated 21 June 2002, an amendment to the Decree 48 by the Government of Vietnam. Hanoi National University, in combination with the Research Center of Phong Nha-Kẻ Bàng National Park, has discovered 1,320 additional species in this park, of which some groups are assessed as specially rare and precious. Biologists have discovered three rare orchid species. Orchids found here include: Paphiopedilum malipoense, Paphiopedilum dianthum, Paphiopedilum concolor. In 1996 IUCN classified these orchid species in danger of extinction in the near future.
2. Faunae
The forest is also home to 98 families, 256 genera and 381 species of vertebrates. Sixty-six (66) animal species are listed in theVietnam's Red Data Book and 23 other species in the World Red Book of Endangered Species. In 2005, a new species of gecko(Lygosoma boehmeiwas) 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. The Gaur and one species of eel have been discovered in this park. Ten new species never seen before in Vietnam were discovered by scientists in this national park.
Saola
The park is home to significant populations of primates in Vietnam, with ten species and sub-species. These include the globally vulnerable Pig-tailed Macaque, Assamese Macaque, Stump-tailed Macaque and White-cheeked Crested Gibbon (Nomascus leucogenys and Nomascus leucogenys siki). The Park is probably home to the largest population of Francois' Langur in Vietnam, including two different forms of the species. The area is highly significant for its population of Hatinh Langur and Black Langur. It is undoubtedly the largest population of these species in the world, and probably the only population represented in a protected area. Other endangered large mammals include the Mainland Serow (Capricornis sumatraensis), Giant Muntjac (Megamuntiacus vuquangensis) and possibly the Saola(Pseudoryx nghetinhensis). The Asiatic Black Bear (Selenarctos thibetanus) and Sun Bear (Helarctos malayanus) are confirmed. Other smaller mammals include Sunda Pangolins (Manis javanica) and the recently discovered Striped hare, called locally "tho van" (Nesolagus timminsii). Ten bat species listed in the IUCN List of Threatened Species have been recorded in this park.
Cyrtodactylus
Of the 59 recorded reptile and amphibian species, 18 are listed in Vietnam's Red Data Book and 6 are listed in the IUCN Red List of Threatened Animals. The 72 fish species include 4 species endemic to the area, including Chela quangbinhensis. The park is home to over 200 bird species, inclusive of several rare birds such as: Chestnut-necklaced Partridge, Red-collared Woodpecker, Brown Hornbill, Sooty Babbler and Short-tailed Scimitar-babbler. There is good evidence for the Vietnamese Pheasant (Lophura hatinhensis) and Imperial Pheasant (Lophura imperialis) species at Phong Nha-Kẻ Bàng area. An initiative survey conducted by Russian and Vietnamese scientists from Vietnam-Russia Tropical Centre (funded by WWF) recorded 259 butterfly species of 11 families. Almost all major butterfly taxa in Vietnam can be found in Phong Nha-Kẻ Bàng park.