The Port of Anacortes is located in the State of Washington's Skagit County on the northern end of Fidalgo Island. About 55 kilometers (34 miles) south of the United States' border with British Columbia in Canada, the Port of Anacortes is some 16 nautical miles (26 kilometers or 16 miles) southwest of the Port of Bellingham. Across the Strait of Juan de Fuca and Puget Sound, the Port of Anacortes is about 122 nautical miles (103 kilometers or 64 miles) north-northwest of the Port of Seattle. The 2010 US Census reported a population of almost 15.8 thousand in the Port of Anacortes and a population of over 116.9 thousand in the Mount Vernon-Anacortes metropolitan area.

The Port of Anacortes began as Ship Harbor in the 1860s. Through the late 20th Century, the Port of Anacortes was best known as home to a fish-processing industry and oil storage facilities, both of which are still important to the local economy. Since the 1980s, the Port of Anacortes has also been a popular recreation and tourism center. The Port of Anacortes is the base for a Washington State Ferries terminal with routes to Lopez Island, Orcas Island, Shaw Island, and San Juan Island as well as to Victoria, British Columbia on Vancouver Island. Skagit County operates a ferry to the residential Guemes Island located about a mile north of the Port of Anacortes.

The area that would become home to the Port of Anacortes, the Fidalgo and Guemes Island area, has been inhabited by humans for more than ten thousand years. Before Europeans arrived, the Samish and Swinomish people lived there. The Samish people lived on Samish, Guemes, and northern Fidalgo Island, and the Swinomish people occupied southern Fidalgo Island, north Whidbey Island, and the Skagit River delta. The Swinomish Reservation was established on southeastern Fidalgo Island in 1873.

Before Europeans arrived in the Port of Anacortes area, the Samish people fished the islands and channels off what is now Skagit County, Washington. While they had winter villages on Fidalgo, Guemes, and Samish Islands, they followed the salmon runs throughout the San Juan Islands during the rest of the year.

The Samish tribe had more than two thousand members in the early 19th Century. After whites arrived, their numbers were reduced to about 150 due to disease and attacks from other tribes. After signing the Point Elliott Treaty in 1847, some of their members moved to the Lummi and Swinomish reservations.

Occupying land with the only fresh water on Fidalgo Island, the Swamish people had been largely pushed off the island by 1912. In 1926, the Samish established a formal constitution and officially became the Samish Indian Tribe. In 1998, they were recognized by the US Government became the Samish Indian Nation with tribal government located in the Port of Anacortes.

Spanish explorers visited the Port of Anacortes area during the late 18th and first half of the 19th Century. In 1791, the Eliza Expedition found and named Padilla Bay and Guemes Island. In 1792, Captain George Vancouver named Deception Pass and Whidbey Island. In 1841, Allan Island, Burrows Bay, Mount Erie and many other sites in the Port of Anacortes area were named by American explorer Lieutenant Charles Wilkes. Throughout that period of exploration, trappers dramatically reduced the local populations of sea otter, beaver, and other fur-bearing species.

In the mid-19th Century, the first settlers arrived and established claims on Fidalgo Island. These first Port of Anacortes residents included trappers, hunters, prospectors, surveyors, and soldiers who settled to become farmers and raise cattle. Several of the settlers married native women. By 1873, there were only eight white women in the Port of Anacortes.

In 1865, Richard and Shadrack Wooten settled at the site of today's Port of Anacortes, Ship Harbor. In 1877, Amos Bowman established a post office, giving the town his wife's maiden name, Anna Curtis. Bowman dreamed that the site would become the western end of the transcontinental railroad (which did not happen). The Port of Anacortes was incorporated in 1891, becoming a center for the lumber and fishing industries.

In the 1890s, the Port of Anacortes became home to the codfish-curing and salmon-canning industries. By the turn of the century, a dozen fish-processing plants provided work for hundreds of people in the Port of Anacortes. While most of these plants closed by the 1960s, Seabearer, Sugiyo, and Trident Seafoods still operate in the Port of Anacortes today.

By the early 1900s, the Port of Anacortes also had a growing lumber industry with five sawmills and six shingle mills. In the first two decades of the 20th Century, several lumber companies were established, including Fidalgo Island's biggest mill. The plywood mill cooperative established by community leaders in the 1930s operated continuously until 1990.

In 1941, the US Navy selected Fidalgo Island for a base that would re-arm and refuel Navy patrol plans to defend Puget Sound. The US Naval Air Station Whidbey Island was commissioned in 1942, and it was an active military installation throughout the rest of World War II. During the Korean War, several Naval Reserve Units were stationed there. Since then, providing residential services for the Whidbey Air Station has been an important part of the Port of Anacortes economy.

Several oil companies established large oil refineries near the Port of Anacortes on Fidalgo Island in the 1950s. Refining is still the largest industry for the area, although fish processing, tourism, and yacht- and ship-building are also important sectors in the Port of Anacortes' modern economy.

The Port of Anacortes is a popular destination for travelers to the San Juan Islands and for recreational boaters. Located off the Strait of Juan de Fuca, the Port of Anacortes is also a popular location for whale watching where the nearby waters are home to three resident pods of Orca and a wide variety of marine life.

In addition to boating, visitors to the Port of Anacortes enjoy camping in Washington Park, an 89-hectare park offering boat launches, camping, and fantastic views of the San Juan Islands. The Port of Anacortes Community Forest Lands is a 1133-hectare area within the city with lakes, meadows, wetlands, and forest as well as about 80 kilometers (50 miles) of trails for hiking and mountain biking. The Port of Anacortes is the western end of the Northern Tier, the Adventure Cycling Association's cross-country bicycle route that originates in Bar Harbor Maine. Rock climbers come to negotiate the cliffs on Mount Erie about seven kilometers (4.3 miles) south of the Port of Anacortes.

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