This from the World Wildlife Fund site:

——————————————-

Until recently the pygmy elephants of Borneo were believed to be a remnant population of a domesticated herd abandoned on the island by the Sultan of Sulu in the 17th century. But a 2003 DNA analysis carried out by WWF and Columbia University proved that the pygmy elephants were genetically distinct from other Asian elephants, thereby recognizing it as a likely new subspecies and emphasizing its conservation priority.

According to the DNA evidence these elephants were isolated about 300,000 years ago from their cousins on mainland Asia and Sumatra. During that period, they became smaller with relatively larger ears, longer tails and straighter tusks.

The evolutionary history of Borneo’s elephants justifies their recognition as a separate evolutionary significant unit (ESU).

——————————————

It sounds as if Borneo (if the DNA tests can be trusted) has not only had elephants historically, but has had them since substantially PRE-history. Genetic isolation dating from 300K years ago indicates that they were on Borneo long before then.

The rest of the story:

http://www.panda.org/about_wwf/what_we_do/species/about_species/species_factsheets/elephants/asian_elephants/borneo_pygmy_elephant/index.cfm