Before white men came, this area was occupied by aborigines from two different groups: Tehuelche on the continent, and Alakalufe on the coast.
The Tehuelche were pedestrian hunters until the arrival of the Spaniards, who introduced the horse, and they became equestrian, and indeed very good riders.
They were nomad, and lived on guanacos, pumas, huemules, and ñandúes, as well as other animals they hunted by means of bows, arrows, and bolas.
They called themselves Tzónekas, what in their language means man, people.
The Alakalufe called themselves Keweshor. They were shorter than the Tehuelche, with robust thorax and abdomen, and short and thin legs. Their main activity was related to the sea. They lived in very primitive sea lion leather cabins, were carnivorous, with a preference to seal and whale meat.
According to evidence, there was no war between the Tehuelche and the Alakalufe, not even a conquering anxiety or a commercial interest. Notwithstanding, according to Father García, in case it had occurred, the only possibility could have been in the area of the present province of Capitan Prat, though the rivers Chacabuco, Baker, and Cochrane, because "the Tehuelche could have arrived to swamp Baker in pursuit of huemules, so abundant in the region".
Around the year 1914, Puerto Aisen becomes the big ships port of the livestock company SIA, and the village starts organizing in the 20s, becomes a town in 1928, and is still at present , head of the insular territory.
The erosion provoked by forest fires, and the drainage of the water through the channels as a result of colonists´ activities to gain grazing lands for their cattle have reduced the port´s potential, being at present only for fishing boats and vessels.
Some historians consider Ferdinand Magellan the discoverer of Aisén, a territory known by the Spaniards as Provincia de Trepanada, visualized from his ship after crossing the Strait on 1st December 1520, when he saw an irregular coast with high cliffs that he called "Tierras de Diciembre".
After some time, in 1553, Pedro de Valdivia sent the expedition of Francisco de Ulloa, the first sailor who arrived to this coast and reached the Taitao Peninsula.
During 1766 and 1767, there are important discoveries in Trepanada. Father José García Alsué went on an exploratory mission south of Palena, where he recognized channels Jacaf and Puyuhuapi while travelling along the river and part of the valley of Queulat in an effort to find the City of Caesars. In the maps he traced, he drew for the first time the fjords of the river Aisén, which he called "Los Desamparados". He reached Golfo de Penas passing through Ofqui istmus.
From 1782 to 1796, the pilot José de moraleda y Montero used maps of Chiloé and Palena to measure and explore the fjords and the river Aisén.
In 1831, Fitz Roy with Charles Darwin initiated a scientific expedition on board of the ships "Adventure" and "Beagle" to travel along the coast of Trepanada during five years. The maps and charts drawn by these two scientists are a fundamental base of southern chartography.
Between 1870 and 1872, Mr. Enrique Simpson Baeza, comandant of the Chilean Marine, arrived at the sector called Alto Baguales, where Patagonian plains start, deducing that it could be the way to the Atlantic.
In 1888 Captain Adolfo Rodríguez recognized swamp Baker, and between 1892 and 1902 the most important discovery and science expeditions were organized by the Chilean government. The German scientist Hans Steffen identified the course of most Patagonian rivers draining to the Pacific, among them, Puelo, Manso, Cisnes, Aisén, Huemules, and Baker, and their inner branches. In 1902, he accompanied the British arbiter Holdich while performing the limiting research between Chile and Argentina as a Chilean representative.
During several decades, the German agricultural engineer Augusto Grosse made numerous explorations in the province of Aisén in search of internal routes and colonizable farms. He was appointed "explorer" by the Ministry of Public Works.