Archaeological excavations reveal that El Nido was already inhabited by humans 12,000-14,000 years ago. The University of the Philippines – Archaeological Studies Program [UP-ASP] in partnership with the University of Washington discovered a 500-1,500 year-old trading community in Sibaltan. There were evidences that Tang Dynasty [618-907 C.E.] traders were frequenting El Nido during that period.

The first recorded name of El Nido was talindak,  the name of a Tagbanua community located at the present day Sitio Langeb-Langeban of Barangay Aberawan. In 1890, it was renamed as Bacuit by the Spaniards. During the Spanish colonization, Bacuit was a just a barrio of the Municipality of Taytay, the capital of the former province of Calamianes. In 1916, Bacuit finally became a municipality. On June 17, 1954, through Republic Act 1140, the town received its present name “El Nido,” after the nests of swiftlets found in the caves of its 250 million year-old limestone cliffs. El Nido is a Spanish word for “The Nest.”

In 1982, a small resort was opened in Pangalusian Island by the Gordon family. It lasted only for several years. It was followed in 1983 by a luxury dive resort in Miniloc Is. owned by Ten Knots Development Corp [TKDC]. In 1984, The Ministry of Natural Resources issued administrative order 518, establishing a 360 sq. km. turtle sanctuary in El Nido. In 1991, the area expanded to the entire Bacuit Bay and became a marine reserve.

After buying Pangulasian from the Gordons, TKDC re-opened Pangalusian Island Resort which was later destroyed by fire in 1998, at the time TKDC was building its third resort in Lagen Is.   In the same year, El Nido-Taytay Managed Resource Protected Area was established. This covers 90,321 hectares of marine and terrestrial protected area. ENTMRPA included 4 barangays from Taytay muncipality.

In 2004, Amazing Race was filmed in El Nido. On the 2nd of April 2006, El Nido laid its first artificial coral reefs in Tres Marias group of islands. The project was funded by Seacology, a group of donors for restoring marine eco-systems in different countries. In 2007, French version of Survivor was filmed in El Nido.