El Nido has been inhabited by humans as early 2680 BC, or even up to 22,000 years ago. This was confirmed by the fossils and burial sites, dating back to the Late Neolithic Age, that can be found in many caves and excavation sites surrounding the municipality, particularly the Ille Cave in New Ibajay. Chinese traders had been regularly visiting the area of El Nido for its edible birds’ nests during the Song Dynasty (960-1279). In fact, El Nido is specifically mentioned in Chinese records as far back 1225. Chau Ju-Kua, a member of the Chinese Royal Family, Trade Commissioner and Superintendent of Customs of the Port of Chuan How wrote about the island, Pa-Lao-Yu or Land of Beautiful Harbors in his book Chu Fan Chi.
The town traces its roots from a small Tagbanwa village called Talindak. Some time in the 16th century, waves of migrants from Cuyo Islands came here to settle. In the 1800s, the Spaniards arrived, and they moved to the part where the present-day Población and Mabini are located. The first Spanish families were the Canovas, Vázquez, Ríos and Rey. In 1890, the Spaniards renamed it as Bacuit. At the time, the center of the town was Cabigsing, then known as Inventario. Chinese families moved into the area about the same period, first settling in Langeblangeban. The first Chinese settlers were named Lim, Chin, Liao, Edsan, Ambao, Que-Ke, Lim Piao, Yu His, Pe Phan and Pe Khen.
During the Spanish colonization of the Philippines, the town was under the jurisdiction of the Municipality of Taytay, which was the capital of the former Province of Calamianes from 1818, and the Province of Castilla, the area of what is now known as northern Palawan, from 1858. It remained part of Taytay until 1916 when it formally became an independent municipality. The new municipality was then known as Bacuit.
Some stunning photos of El Nido