These endangered species includes the Sunda pangolin (Manis javanica), Bengal slow loris (Nycticebus bengalensis), Germain's langur (Trachypithecus germaini), Indian hog deer (Axis porcinus), dhole (Cuon alpinus), clouded leopard (Neofelis nebulosa), fishing cat (Prionailurus viverrinus), Asian elephant (Elephas maximus), and pileated gibbon (Hylobates pileatus).

The area was expected to hold a large number of species, since the Cardamom Mountains are home to many, there are a broader variety of ecosystems to be found in Botum Sakor.

There are a number of other threatened or near-threatened birds here too, like green peafowl (Pavo muticus), lesser adjutant (Leptoptilos javanicus), Oriental darter (Anhinga melanogaster), great pied hornbill (Buceros bicornis) and grey-headed fish eagle (Haliaeetus ichthyaetus).

The relatively high percentage of Nymphalidae species in Botum Sakor are, in addition to other factors, reflecting that the habitats are indeed disturbed by excessive clear cutting and logging.

[12] After establishing the Botum Sakor National Park in 1993, the Government of Cambodia apparently decided, that a large part of the land should be used for various agro-industrial and construction projects.

How land is exploited, sold and leased in Cambodia is notoriously murky,[13] but below is a list of well documented projects in relation to the park: In November 1998, a concession agreement was signed with the Chinese company The Green Rich Co., Ltd. to plant, grow and harvest oil palms, fruit trees and acacia in a 60,200 ha (602 km2) area.

[15][16] In August 2009, a concession agreement was signed with Koh Kong sez Co., Ltd., to initiate a large scale agro-industrial project in a 9,977 ha (99.77 km2) area.

[17] In April 2010, a concession agreement lasting 90 years was signed with the Cambodian company L.Y.P Group Co., Ltd. To construct Tapioca plantations in a 4,097 ha (40.97 km2) area.

[20][21] In July 2011, a concession agreement was signed with the company Sinimexim Investment Co., Ltd. to construct rubber plantations and conduct unspecified agro-industrial business activities in a 4,280 ha (42.80 km2) area.

Landsat satellite images, journalistic investigations and activist reports clearly shows how large areas have been clear-cut at an accelerated pace in the concessions since 2008.

[25] There is now substantial evidence, that the criminal practices of illegal logging on the premises of the national park, has become a problem once again in the last few years and at an alarmingly accelerated pace even.

Satellite images (Landsat and Envisat), journalistic investigations and activist reports shows how the formerly densely forested interior has been thinned to an extent, that almost all of Botum Sakor National Park has been directly affected.

[26][27] There seems to be a number of reasons for the new illegal logging practices and various groups participate, spanning from opportunistic locals, some of the companies involved in the concessions (see above) and organized criminal syndicates.

Some of the logged timbers are rosewood and various threatened hardwood species used in luxury buildings and for expensive furniture, but also plants like the saffrol laurel tree (Cinnamomum parthenoxylon, a member of the cinnamon tree genus) and yellow vine[28] are being cut and collected to make psychoactive drugs like ecstasy for south-east Asian traditional medicine and other purposes.