International scientists and environmentalists rank Samar as one of the biodiversity-rich regions in the world. For birds alone, Samar is a critical habitat to some 197 species of which 16 are endangered. The island is also home to plant and animal species that cannot be found elsewhere on earth, hence, it is one of 18 plant diversity centers. Twelve endemic trees found on the island are included in the World List of Threatened Trees. Samar has the largest remaining contiguous lowland forests in the country. Recognizing the need to protect the forests the government established the Samar Island Forest Reserve covering a total area of 360,000 hectares in 1996 and, subsequently, the Samar Island National Park comprising 333,000 hectares in 2003. The SINP aims to preserve the country's largest contiguous lowland tropical rainforest.

Overlapping with these declared protected sites are old logging concessions and mining reserves and applications, which pose the most serious threats to the rich biodiversity and environmental integrity of the island. Logging had been operating in Samar until the floods of 1989 that prompted the government to impose a logging moratorium in Samar. Allowing the resumption of logging and mining raises ecological concerns, such as loss of biodiversity and environmental destruction, which constitute a primary reason for the strong opposition to the DENR's decision to uphold the 95,770-hecatare timber concession of San Jose Timber Corporation in Samar inside the 330,000-hectare protected Samar Island Nature Park. For the moment the logging has been halted.