Ben En National Park is situated at the transition between the broad coastal plain of Thanh Hoa/Nghe An provinces and the peak of northern Truong Son mountain range. Topography has formed a rich diversity in flora and fauna. Many of the unique species which can be found in famous Truong Son mountain range are also native to Ben En.

Flora 
Ben En has two major forest ecosystems, limestone forest and forest on other soils.

Overall, in Ben En also the following vegetation types can be found :

• Tropical evergreen limestone forest 
• Tropical evergreen lowland forest on other soils
• Bamboo forest mixed with timber trees
• Plantation forest
• Agricultural land

Survey results in 2007, 2008 have recorded 6 phyla with a total of 1,389 vascular plants species belonging to 650 genera and 173 families. 

Three species are new to the flora of Vietnam:

• 1. Glyptoetalum sclerocarpum(Kurz) M.A Lawson
• 2. Myristica yunanensisY.H. Li
• 3. Timonius arboreaElmer.

29 plants in Ben En are listed as endangered on the 2006 IUCN red list, 45 species are listed in the Vietnam Red Book of 2007. Amongst them are e.g. Sindora tonchinensis, Hopea hainanensis or Annamocarya sinensis.

Fauna 

A survey published in the year 2000 recorded 1,004 animal species in Ben En, which is 17.31% of Vietnam's total fauna. This includes 91 species of mammals, 261 species of mammals birds, 54 species of reptiles, 31 species of amphibians, 68 species of fish and 499 species of insects. 

In Ben En 93 rare animal species were recorded which are listed in Vietnam's Red Book such as White-Cheeked Gibbons, Stump Tailed Macaques, Pygmy and Slow Lorises, Pheasants or Bears.