Before being called Puerto Aysén, this territory was dwelled by natives: the Tehuelches on the continent and the Alacalufes on the littoral.
The Tehuelches used to refer to themselves as tzónecas (people). They fed on cougars, guanacos and rheas they used to hunt and they were nomads. On the other hand, the Alacalufes or Keweshor differed from the Tehuelches because they were sturdier and had shorter legs. Generally, they inhabited cabins made with wolf leather and they were carnivores. According to evidence existing today, these groups of natives did not confront.
In 1914, the local population began to be organized in the territory as a result of the construction of a wharf by the livestock company known as SIA. Afterwards, in 1928, this place was turned into a municipality.
Some historians consider that it was Ferdinand Magellan who discovered Aysén when he saw an uneven littoral and hills he came to call Tierras de Diciembre (December Lands) after crossing the strait on December 1st., 1520. Later on, in 1553, Pedro de Valdivia sent Francisco de Ulloa on an expedition that turned the latter into the first sailor of the Aysén lands.
In 1766, José García Alsué went on an exploration mission from Palena in the south and got deep into the river to tour part of the Queulat. Alsué charted the fjord of the Aysén River for the first time and named it Los Desamparados (The Helpless). In the late 1700s, José de Moraleda was in charge of charting the territories of Chiloé and Palena. He measured and explored the fjords of the area. By 1831, Fitz-Roy embarked upon a scientific adventure that took five years in the company of Charles Darwin. They toured the coasts of Trapananda and chartered the area. Their work was an essential element for the development of southern maps.
Commander of the Chilean Navy Enrique Simpson Baeza arrived in the region known as Alto Baguales between 1870 and 1872. In 1888, Captain Adolfo Rodríguez recognized Baker Marshland.
History also goes that between 1892 and 1902, more important scientific expeditions were sent by the Chilean government, which commanded this task to a German named Hans Steffen. This scientist managed to identify the course of most Patagonian Rivers ending at the Pacific Ocean: the Puelo, the Manso, the Cisnes, the Aysén, the Huemules and the Baker. Besides, Steffen also accompanied an English arbitrator called Holdich, who carried out all the expert reports regarding limits between Chile and Argentina in 1902.
Last but not least, it is also known that German agricultural engineer Augusto Grosse Ickler (who was hired as an "explorer" by the Department of Public Works) carried out a deep search for several decades in the Province of Aysén for inner roads and fields likely to be colonized.