Modern humans, Homo sapiens sapiens, made their appearance in the Philippines earlier than 50,000 years ago, and part of the population, the Mamanua, still exist in the northeastern Mindanao. Toward the end of the Ice Age, the sea started to rise with the melting of the ice caps, beginning from about 10,000 to 30,000 years ago. This is also the period when the Negrito populations of the Philippines made their appearance, passing through the remaining vestiges of the disappearing land bridges.

Located in Lipuun Point, on the central and western side of Palawan, overlooking the South China Sea, Tabon Cave is just one of the many caves collectively known as the Tabon Caves. Its name comes from the Philippine Mound Builder, a megapod bird known locally as tabon since it digs deep into the ground to bury its eggs. This bird nested deep into the guano layers of the floor of Tabon Cave, disturbing the cultural layers. The Tabon Cave complex is 138 hectares of rugged cliffs and deep slopes, discovered by an American, the late Dr. Robert B. Fox, and his team of archaeologists from the National Museum in 1962. Excavations were done from 1962 to 1970.

Of the 200 caves found in Lipuun Point, only 29 caves, including Tabon Cave, were fully explored and found to have been used for habitation and/or burial sites by ancient people. Tabon Cave yielded an important archaeological find – fossil human bones tentatively dated 22,000 to 24,000 years ago, composed of the skull cap, mandible and dentition of the Tabon Man, who was actually a woman. It was also in this Cave that the jaw bone of an orangutan was found, evidencing the presence of a land bridge that connected Palawan to Borneo. Tabon Cave is periodically dry, and is well lit throughout the day, especially in the afternoon, since it faces west.

Because of its importance to Philippine history and heritage, the site was declared a Museum Reservation Site, by virtue of Presidential Proclamation No. 996 in 1972, by the Philippine Government. Out of the 29 explored caves, only three caves are available or open for visitors, and are currently being maintained and managed by the National Museum.