Prior to European settlement, the islands were part of the traditional area of the Central Coast Salish, which based on language consisted of five groups: Squamish, Halkomelem, Nooksack, Northern Straits (which includes the Lummi dialect), and Clallam. Exploration and settlement by Europeans brought smallpox to the area by the 1770s. In 1843, the Hudson's Bay Company established Fort Camosun at nearby Vancouver Island.
The U.S.-Great Britain treaty forced by President Polk in 1846 established the 49th parallel as the boundary between Canada and the U.S., except in the San Juan archipelago. While both sides agreed that all of Vancouver Island would remain British, the treaty wording was left vague enough as to put the boundary between modern-day Gulf Islands and San Juan Islands in dispute. Conflicts over this border led to the Pig War in 1859. Skimishes continued until the boundary issue was eventually placed in the hands of the Emperor of Germany for arbitration. The border was finally established in 1872.
The names of the separate islands are, in alphabetical order: Crane Island, Decatur Island, Lummi Island, Obstruction Island, Orcas Island, San Juan Island, Shaw Island, Spieden Island and Waldron Island.