Biologists had known about the unique orangutan population, which is nestled within the Tapanuli district in North Sumatra, since 1997.
With so few individuals, the new species is now considered the most endangered great ape on the planet, and there are fears it could die out within the lifetime of its discoverers. Orangutans typically do not live in high altitude areas. This is the first great ape species to be described by scientists in almost 90 years.
A team led by experts at the University of Zurich in Switzerland has now established that those orangutans are a distinct third species from the two established species - the Bornean and the Sumatran orangutans, the Daily Mail noted.
Orangutans are native to Indonesian forests, though their populations have been in steady decline in recent years due to rampant deforestation.
Firstly, they used the skull of a specimen killed during what they describe as a "human-animal conflict" to compare head and jaw characteristics with those of 33 adult male orangutans.
The Tapanuli orang utan species became isolated from its Sumatran relatives about 10,000 to 20,000 years ago, eventually settling in the Batang Toru forest.
"It isn't an everyday event that we find a new species of great ape, so indeed the discovery is very exciting", said Michael Krutzen from the University of Zurich.
They also found that the Tapanuli's orangutan's lineage was ancient - between 3 million and 3 1/2 million years old - and that they appeared to be direct descendants of the orangutan ancestors that crossed into what is now Indonesia and Malaysia from mainland Asia.
Meanwhile Bornean and Sumatran orangutans separated only 700,000 years ago. Orangutan populations are threatened by deforestation for agricultural use, and P. tapanuliensis is no exception.
Wiratno, the director general of conservation of natural resources and ecosystems at Indonesia's Forestry and Environment Ministry, told a news conference in Jakarta that most of Batang Toru forest was designated as protected in December 2015. Forests in the Batan Toru ecosystem are now being logged to make way for palm oil plantations, and there's even a plan to raise a new hydroelectric dam which could also impact the habitat of Tapanuli orangutans.
It is the most endangered of the now seven known species of great apes.
The team notes that we will need to quickly implement conservation measures to ensure that illegal logging, road construction, and other human threats don't impact the long-term survival of the species.
Erik Meijaard of the Australian National University said: "Great apes are among the best-studied species in the world". That makes the Tapanuli population extremely vulnerable and the great ape species at the greatest risk of extinction.