The Borneo elephant, also called the Borneo pygmy elephant, is a subspecies of Asian elephant that inhabits northeastern Borneo, in Indonesia and Malaysia. Its origin remains the subject of debate. A definitive subspecific classification as Elephas maximus borneensis awaits a detailed range-wide morphometric and genetic study. Since 1986, Elephas maximus has been listed as Endangered on the IUCN Red List as the population has declined by at least 50% over the last three generations, estimated to be 60–75 years. The species is pre-eminently threatened by habitat loss, degradation and fragmentation.

The Sultan of Sulu introduced captive elephants to Borneo in the 18th century, which were released into the jungle. Comparison of the Borneo elephant population to putative source populations in DNA analysis indicates that the Borneo elephants are derived from Sundaic stock and indigenous to Borneo. The genetic divergence of Borneo elephants warrants their recognition as a separate evolutionarily significant unit.

Due to their small size, gentle nature and relatively large ears, they have been dubbed “pygmy” elephants. Less than 1,500 Borneo Pygmy elephants (Elephas maximus borneensis) are found, mostly in the Malaysian state of Sabah. This makes Sabah home to the world's smallest known sub-species of elephants.

Elephants were appropriate gifts from one ruler to another, or to a person of high standing, and it was customary to transport them by sea. In about 1395, the Raja of Java gave two elephants to the ruler Raja Baginda of Sulu. These animals were reputedly the founders of a feral population at the western end of Borneo. When in 1521 the remnants of Ferdinand Magellan’s circumnavigation of the Earth reached Brunei, the chronicler of the voyage recounted that the delegation from the flagship Victoria was conveyed to and from the ruler’s palace on elephants caparisoned in silk. This custom had been discontinued by the time later visitors arrived in Brunei in the 1770s, who reported wild-living elephant herds that were hunted by local people after harvest. Despite the early records of royal elephants in Brunei and Banjarmasin, there was no tradition of capturing and taming local wild elephants in Borneo.[2]

The arrival of elephants in the north Kalimantan region of Borneo coincides with the rule of the Sultans of Sulu over Sabah. The Sultanate of Sulu enjoyed peaceful ties with the Hindu Sultanate of Java. As a token of appreciation, the rulers of Java sent their elephants to Sulu, much as they have sent Javanese elephants to the Sultanate of Maguindanao, which also partly gives the reason why skeletal remains of small elephants are found in Mindanao, south Philippines. The Sultan of Sulu and his family shipped some of their prized Javanese elephants to northeast Borneo due to lack of land and for the elephants to help in hauling logs out of the forest to create fast and long ship vessels. When this lease was signed, most of these timid.