Sparsely-populated Halmahera's fortunes have long been closely tied to those of the smaller islands of Ternate and Tidore, both off its west coast.

In 1999 and 2000, Halmahera was the site of violence that began as a purely ethnic dispute between residents of (mainly Christian) Kao and (entirely Muslim) Malifut sub-districts and then took on a religious nature as it spread through much of the North Moluccas, called the Maluku sectarian conflict.

In June 2000, about five hundred people were killed when a ferry carrying refugees from the fighting on Halmahera sank off the northeast tip of Sulawesi island.

Today, much transportation to the rest of Indonesia is through connections on the provincial capital, Ternate island although Tobelo, the largest town on Halmahera, also has direct ferry and cargo sea links to Surabaya and Manado.

[citation needed] Particularly, since the inauguration of the first ever directly elected Bupati (Regent or District Head), Tobelo is undergoing rapid development and is aiming at rivaling Ternate's historical dominance.

Only Ternate Municipality, and Morotai, the Sula Islands and Taliabu regencies do not include any part of Halmahera.

[8] Uncontacted members are being threatened by a massive Indonesian mining project to produce nickel for electric car batteries.

[12] It was in February 1858, on the island of Ternate (or perhaps while on Halmahera itself), between bouts of fever, that Wallace came to the idea of natural selection via the survival of the fittest.