Although one of the newest provinces of the country, settlements in Dinagat Islands were already present during the Spanish regime as a result of migration of people from nearby provinces of Bohol and Leyte. The so-called mystical province played an important role in the country's history, particularly during World War II.  Adding to the historical significance of the province is the foundation of the Philippine Benevolent Missionary Association by Ruben Ecleo, Sr.

The municipality of Dinagat is the oldest community in the province. In the early days, a story was told that a stranger reached the place in search of greener pastures. He approached a native and asked what the inhabitants do for a living. The natives said that they farm and fish to live. The stranger's interest in fishing prompted him to inquire where they fish, and the native replied and pointed to a place saying ? ?dinhi niini na dagat? (here from this bountiful waters). Since then, the place was called Dinagat.

The municipality was formally established in 1855. It occupies the territorial boundaries of the whole island. From 1890 to 1990 its boundaries were gradually reduced giving rise to six municipalities ? Loreto, Cagdianao, Libjo, Basilisa, Tubajon and San Jose.

Loreto became a Spanish pueblo on September 4, 1890 under the supervision of Governor General Manuel Sanchez by the virtue of Direccion General No. 30. It was originally called "Mabua" because of the ever-foaming river that runs right into the center of the community. It was named ?Loreto? in 1881 by the Spanish priest who frequents the town, in honor of the wife of the Alcalde Mayor of the Province of Surigao.

The province was the site of the historic Battle of Surigao Strait during the Second World War. The Municipality of Loreto became the entry point of the American Liberation Forces on October 17, 1944. It was on this shore that the 6th Ranger Battalion of the 6th U.S. Army under Col. Mucci landed at Sitio Campinta of Barangay Panamaon, Loreto. It was during this landing that the first American flag flew on Philippine soil.  They named the place "Black Beach No. 2."

The northern part of the island served as a refuge of the American soldiers, while the western border was the camp site of the Japanese Forces. Capsized vessel structures are still found today in the waters of Basilisa.

On December 23, 1959 Cagdianao was created into a municipality under Executive Order No. 367. Its name came from the Spanish word "Cada dia linao" meaning everyday peaceful and calm. However some scholars say that its name came from the Visayan word "Taga Danaw" meaning the lake people.

Libjo was created into a municipality and named Albor on February 29, 1960 under Executive Order No. 381. It was taken from the municipalities of Dinagat and Loreto. "Albor" came from the surname of the mayors of Loreto and Dinagat - Alfaro and Borja. It was renamed as Libjo on June 17, 1967. The name came from the word "Liboo" which is a kind of mussel clam.

In 1965, Ruben Edera Ecleo Sr. founded the Philippine Benevolent Missionaries Association (PBMA) at Sitio Puyange, now Poblacion San Jose. It is a non-sectarian organization bounded by a strong spirit of brotherhood. Not long after that, members from all over the country migrated in the island to be in constant association with their founder.

Meanwhile, Basilisa became a municipality in June 17, 1967 under Republic Act No. 4986. It was then named as Rizal, after the country?s national hero. The municipality was renamed as Basilisa on June 21, 1969 under Republic Act. No. 5775.

Tubajon, which was once a barangay of Loreto became a municipality in June 21, 1969 under Republic Act No. 5643. A local folklore states that during the Spanish regime, a banca boarded with Guardia Civils landed in the shores of Tubajon in search of a criminal. One of them came across a river and saw a man pounding leaves, curious, he asked the man "What will you do with it?". The man answered "Akong Tubajon ang suba aron sayon dakpon ang mga isda" (I will poison the river with Tuba leaves so that the fishes could be easily caught). When the man returned to the group, he narrated everything he saw and heard from the native to his companions. From then on, the place was called Tubajon.

The newest municipality is San Jose. It became a municipality on November 15, 1989 under Republic Act No. 6769. The town was named in honor of Jose Ecleo who was its pioneer and father of the late renowned mayor of the municipality of Dinagat, Hon. Rubern Edera Ecleo Sr. The town is the seat of the PBMA.

Dinagat Islands was part of the First District of the province of Surigao del Norte until it became a separate province in October 2, 2006 as stated in Republic Act No. 9355 or the Charter of the Province of Dinagat Islands.

Last January 2007, Surigao del Norte Governor Robert Lyndon Barbers inducted the interim officials whose term ends after the newly elected provincial officials assume office after the May 14, 2007 elections.

The interim officials were Geraldine Ecleo-Villaroman as Governor, Elvis A. dela Merced as Vice Governor, Provincial Board Members Merlinda B. Lagroma, Norberto A. Sarita Sr., Mario P. Menil, Zacarias N. Vales, Gracelyn B. Ecleo, Nilo P. Gulfo, and Rolizareth T. Ladaga. They took oath at the Municipal Cultural Center of San Jose.

^{Source: Province of Dinagat Islands}