In Portuguese Timor, the then district had the same boundaries as the present municipality; however its capital was at Vila Armindo Monteiro, which is now called Bobonaro.

The Indonesian checkpoint is located in Mota'ain in Belu Regency, Nusa Tenggara Timur Province.

Another minor border crossing checkpoint is maintained by the Immigration Service of East Timor within this municipality at Tunibibi near Maliana.

The municipality had been a popular destination in Timor, due to its mountains and hot springs, but it suffered much violence in the war for independence.

Balibó, located about 10 miles from the Indonesian border, was estimated by Human Rights Watch to be 70% destroyed during the militia violence that preceded the referendum for East Timorese independence.

It was also the site of the killing of five Australian-based journalists (the Balibo Five) by Indonesian forces on 16 October 1975 during an incursion by Indonesia into what was then Portuguese Timor.

On 29 May 2001, former members of Dadaras Merah Putih who had become indebted to a cross border gambling ring in Maubusa, in retaliation they threw around four grenades over the Loes River from the Indonesian side towards the market in the East Timorese side killing five, one of the leaders of the gambling ring were killed, but the other four were uninvolved, over 40 others were wounded in the attack.