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The Chilkat River Valley takes its name from the Chilkat Indians who originally settled here. It is also home to approximately 3500 bald eagles who gather at the junction of the the Chilkat and Tsirku rivers from October to February. It serves a corridor from its port village of Haines at its southern tip to Canada on its northern border. The valley has long served as a trade corridor between the sea to the interior. The Ganaxtedih and Daklawedih Ravens, local Indian tribes owned trading trails to the Yukon Gunana tribe ("Stick Indians") over Chilkat Pass. The area around present-day Haines was called "'Dtehshuh" or "end of the trail" by the Chilkat group of Tlingit. It received this name because they could portage (carry) their canoes from the trail they used to trade with the interior, which began at the outlet of the Chilkat River, to Dtehshuh and save 32 km (20 miles) of rowing around the Chilkat Peninsula.

The first European, George Dickinson, an agent for the North West Trading Company, settled at Dtehshuh in 1880.

In 1881, the Chilkat asked Sheldon Jackson to send missionaries to the area. S. Young Hall, a Presbyterian minister, was sent. He built the Willard mission and school at Dtehshuh, on land given the church by the Chilkat. The mission was renamed Haines in 1884 in honor of Mrs. F. E. Haines, the chairwoman of the committee that raised funds for its construction.

The boundary between Canada and the U.S. was then only vaguely defined (see Alaska boundary dispute). There were overlapping land claims from the United State's purchase of Alaska from Russia in 1867 and British claims along the coast. Canada had requested a survey after British Columbia united with it in 1871, but the idea was rejected by the United States as being too costly given the area's remoteness, sparse settlement, and limited economic or strategic interest.

The Klondike Gold Rush of 1898-1899 changed the region greatly. The population of the general area increased enormously and reached 30,000, composed largely of Americans. Haines grew as a supply center, since the Dalton Trail from Chilkat Inlet offered a route to the Yukon for prospectors. Gold was also discovered just 36 miles from Haines in 1899 at the Porcupine District. During this time the name Haines came into use for the area around the mission and not for just the mission itself.

The sudden importance of the region increased the urgency of fixing an exact boundary. There were reports that Canadian citizens were harassed by the U.S. as a deterrent to making any land claims. In 1898 the national governments agreed on a compromise, but the government of British Columbia rejected it. U.S. President McKinley proposed a permanent lease of a port near Haines, but Canada rejected that compromise.

The economy continued to grow and diversify. Four canneries were constructed around the mission by 1900. However, the completion of the White Pass and Yukon Route railway in neighboring Skagway that same year led to the Dalton Trail's eventual abandonment and Haines' economic decline.

In 1903, the Hay-Herbert Treaty entrusted the border decision to arbitration by a mixed tribunal of six members, three American and three Canadian/British, who determined in favor of the United States, resulting in the present-day border.

Fort William H. Seward, a United States Army installation was constructed south of Haines in 1904, on property donated by the mission from its holdings. In 1922, the fort was renamed Chilkoot Barracks. It was the only United States Army post in Alaska before World War II. During World War II, it was used as a supply point for some U. S. Army activities in Alaska. The fort was deactivated in 1946 and sold as surplus property to a group of investors (Ted Gregg, Carl Heinmiller, Marty Cordes, Clarence Mattson, and Steve Homer) who called it Port Chilkoot, thus forming the Port Chilkoot Company. In 1970, Port Chilkoot merged with Haines into one municipality. In 1972, the fort was designated a National Historic Landmark and the name, Fort William H. Seward, was restored. In 1943 the Haines Highway was extended north from Haines to meet the Alcan Highway. The Haines House, a Presbyterian foster home for children operated between 1921 and 1960 when it was demolished due to lack of funding.

The last of the four canneries closed in 1972 due to declining fish stocks. Logging and sawing timber has been an industry around Haines but has declined also in recent years. Tourism is now an important source of income in the community.

The borough seat, Haines, has a somewhat moderate climate for Alaska, with the lowest temperature (-17°F) in 1917 and the highest temperature (99°F) recorded in 1915. Currently the Borough contains approximately 2400 residents.

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