Haines was established as a mining supply and fishing port. Gold seekers swept up in the Klondike rush at the end of the 19th century arrived at the port and then walked northward, following the well-beaten Dalton Trail. They brought everything they owned with them, including farm animals. They felt they had no choice, they were leaving everything they knew and venturing into an unknown wilderness. The narrow and very scenic modern Haines Highway follows the original trail route.

As the Klondike Rush slowed, people began to notice that the southeast Alaskan frontier was still wild and open. By 1901, the continuing US-Canadian border dispute prompted the American government to establish a military base at the missionary settlement at Haines. The Presbyterian Church had established the town in 1881 at the invitation of the local Tlingit people. The church donated 100 acres of property adjacent to Haines to establish a military fort. Named to honor William H. Seward, Fort Seward was a frontier outpost. Work began in 1903, when men, using only horses, mules and oxen, began clearing the land by hand. Its remoteness and primitive environment classified it as "foreign duty" for soldiers, who earned double credit for each year at the site. At the end of the border dispute the fort was decommissioned as "surplus army property."

Haines is just a short distance from Skagway, but it is another world. The tiny community is known for its beauty and its accessibility to Alaska's most impressive indigenous wildlife. Lynn Canal, North America's longest fjord, narrows near the port. Haines is also important in Alaskan history as the birthplace of the official state song, "Alaska's Flag". The pretty and untamed surrounding region is still favored among outdoor enthusiasts.