The subspecies was feared to be functionally extinct, with only one individual, a female named Pahu, surviving in captivity, and held in the state of Sabah.

However, in March 2016, a young female rhino was captured in East Kalimantan (in the Indonesian portion of Borneo), providing evidence of their continued existence.

The Bornean rhinoceros has the darkest skin of the Sumatran rhinos, and the fur of calves is much denser, but it becomes darker and more sparse as the animal matures.

[6] A recently captured specimen and video evidence from camera traps have confirmed their continued presence in East Kalimantan,[2][7] now believed to hold the entire wild population.

[3] Today, the Bornean rhinoceros, like the Sumatran rhino, lives in hot, humid closed canopy rainforest.

In April 2007, it was announced that a camera trap in Sabah had captured footage of a Bornean rhinoceros eating and investigating the equipment.

[6] Poachers continue to be one of the largest threats to the Bornean rhinoceros and local wildlife patrols were increased in November 2015 to protect the remaining population.

[9] Beginning in the 1960s, large-scale logging for international consumption heavily degraded or completely cleared much of Borneo's rainforest.

[2][9] The WWF plans to create a new sanctuary for Bornean rhinos on 200 ha (490 acres) of the 4,561 ha (11,270 acres) Kelian Protected Forest (site of the former Kelian Mine) and move the remaining wild rhinos there to create a larger protected breeding population.

The female rhino (named Najaq) was captured in preparation for this, and was moved to a temporary enclosure with plans to airlift her to the protected forest.

However, a few days after her capture, Najaq died from an infection on her leg, believed to be caused by a poacher's snare trap.

In February 2014, a decision was made to send Tam to the Cincinnati Zoo and Botanical Garden to breed with its female Western Sumatran rhinoceros, Suci.

[12] Puntung fell ill and was euthanized in May 2017, so in late 2018 a new female rhinoceros, named Pahu, was captured for the captive breeding program.