An worldwide team of researchers from 34 institutions, led by anthropologist Alexander Nater of the University of Zurich in Switzerland, pursued two lines of evidence to determine if the ape colony was different enough from the two already acknowledged orangutan species - known as the Bornean and Sumatran - to be defined as a third.
Orangutans are native to Indonesian forests, though their populations have been in steady decline in recent years due to rampant deforestation.
The research is based on analysis of the skeleton of an adult male killed in a conflict with villagers, a genetic study indicating the population's evolutionary split from other orangutans occurred about 3.4 million years ago, and analysis since 2006 of behavioral and habitat differences.
The team argues that the orangutans they've found in the small forest of Batang Toru are "a geographically and genetically isolated population" living further south from the existing range of Sumatran orangutans.
To verify the morphological and genetic examination, the team employed a complex computer model which revealed that the Tapanuli population must have been isolated from other Sumatran populations of orangutans for least 10,000 to 20,000 years.
"The Batang Toru orangutans appear to be direct descendants of the initial orangutans that had migrated from mainland Asia, and thus constitute the oldest evolutionary line within the genus Pongo", said Alexander Nater, researcher at the Unversity of Zurich.
"It is the first declaration of a new great ape species in about 100 years", Dr Ian Singleton, co-author of the study and director of the Sumatran Orangutan Conservation Programme, told AFP.
It's quite exciting to hear about the discovery of a new great ape species in the 21st century. Orangutan populations are threatened by deforestation for agricultural use, and P. tapanuliensis is no exception.
"It is imperative that all remaining forest be protected and that a local management body works to ensure the protection of the Batang Toru ecosystem", Novak said.
"Great apes are among the best-studied species in the world", said Erik Meijaard, a researcher at the Australian National University. "Humans are conducting a vast global experiment, but we have near-zero understanding of what impacts this really has, and how it could ultimately undermine our own survival".
"It's very worrying", said Prof Wich, "to discover something new and then immediately also realise that we have to focus all of our efforts before we lose it".
It is the most endangered of the now seven known species of great apes. That makes it the most endangered great ape in the world, the researchers wrote.