Before the armed rebellion of the MNLF in the early 1970s, Bongao was merely a backwater village ruled by the prominent noble Halun family, who used to own about three-quarters of the island. The capital of the province was Bato-Bato in the mainland situated in a cove with deep waters suited for anchors of the Philippine Navy. At the height of the armed rebellion and fearing that the provincial capitol might be overrun, the government transferred it to Bongao. The white-washed, Taj Mahal-inspired provincial capitol building is located on a hill overlooking the bay and the whole town to the North of the Island against the backdrop of Mount Kabugan and the famous Bud Bongao (Bongao Peak).
The transfer of the seat of government ushered the rapid development of the island as the southernmost center of commerce and trade. Suddenly, the population swelled as individuals (and their families) who are in government service moved to the town.
 Cultural diversity
Today, Bongao is a minuscule cosmopolitan that is becoming a model of multicultural society. In downtown Bongao, there are mosques for the majority Muslim population, a Catholic church, a church for Protestant inhabitants, a Chinese temple, a church for the Iglesia ni Cristo, a church of the Seventh-Day Adventist and a Baptist church. There is also a local congregation of Jesus is Lord (JIL) of one-time presidential aspirant Pastor Eddie Villanueva.
The main thoroughfare is Datu Halun St. where the Town Hall is situated. Poblacion is the commercial hub. Most of the businesses here are owned by local people that were former sea pirates. Due to its relative peace and order situation, recent migrant Chinese from Zamboanga have also open business.
Banks operating in Bongao include Land Bank of the Philippines, Philippine National Bank, and Allied Banking Corporation. Quedancor, a government owned investment company, has recently opened business.
The Midway Plaza Mall, a new 2-storey retail center, is the first shopping mall in Tawi-tawi (and the whole of ARMM) opened in April 2010.
Bongao is home to the Mindanao State University - Tawi-Tawi College of Technology and Oceanography (MSU-TCTO), Tawi-Tawi State Agricultural College (TSAC), Mahardika Institute of Technology (MITI), Abubakar Learning Center Foundation College (ACLC), Tawi-Tawi School of Midwifery (TSF). The first two are government owned state colleges, while the last three are privately owned. There are several secondary high schools in Tawi-Tawi such as the MSU TCTO - Science High School, MSU TCTO Preparatory High School, Tawi-Tawi School of Arts and Trade, Notre Dame of Bongao, and so on.
Bongao is politically subdivided into 35 barangays.