[4] In 2008 the government of Chile agreed with the Alfaguara Project's request to establish a whale sanctuary following a poll in which 98% of citizens voted in favor.

It has been assisted by the Rufford Maurice Laing Foundation, Global Ocean and the Mohamed bin Zayed Species Conservation Fund.

The relatively small and isolated population remaining near the Chiloé is threatened by the risk of collision from increasing volumes of shipping, noise and pollution from a Norwegian salmon farming operation and possibly from rising ocean temperatures leading to changes in the food species available to the whales.

Possibly, the region is functioning as the most important forging area for critically endangered southern right whales[7][8] that face near extinction in the nation.

The coastal community has been involved in whale spotting and in developing responsible marine ecotourism, thus contributing to the conservation program while benefiting from it economically.

[3] Three islands about 300 metres (980 ft) off the Puñihuil beach are important breeding sites for Magellanic and Humboldt penguins in the summer months between September and March.

Following a study by the Alfaguara Project the ecotourism boat operators agreed to work together as an association, reducing the number of penguin-watching trips to the islands so as to maximize net income.