Archaeological evidence puts human presence on and around the Cedar Keys at 12,000 years, based on Paleo-period arrowheads and spear points collected by local historian St. Clair Whitman and now displayed at Cedar Key Museum State Park. A dig at Shell Mound, north of Cedar Key, uncovered artifacts dating to 500 BC buried in the upper layers of an ancient midden. The only ancient burial found in Cedar Key proper was a 2,000-year-old skeleton discovered in 1999. In 1801, followers of William Augustus Bowles -- a self-declared "Director General of the State of Muskogee" -- built a watchtower near the islands before Spanish forces destroyed it the following year. Before the First Seminole War, British agents Alexander Arbuthnot and Robert Ambrister used the Cedar Keys to deliver supplies to the Seminoles, and the islands may have served as a refuge for escaped slaves in the early 1820s.

During the Second Seminole War, the U.S. Army established Fort No. 4 on the mainland adjacent to the Cedar Keys. General Zachary Taylor requested the islands be reserved for military use, and General Walker Keith Armistead ordered a hospital built on Depot Key, which became the Army's headquarters in Florida. On nearby Seahorse Key, Cantonment Morgan served as a troop deployment station and holding facility for captured or surrendered Seminoles awaiting forced removal westward. Then on October 4, 1842, a hurricane with a massive storm surge struck the Cedar Keys, destroying Cantonment Morgan and devastating Depot Key. Seminole leaders who had been negotiating their surrender at Depot Key refused to return after the storm. Colonel William J. Worth declared the war over in August 1842, and the Army abandoned the islands.

Settlement came quickly after the Armed Occupation Act of 1842 opened the islands to homesteaders. Augustus Steele, the U.S. Customs officer for Hillsborough County, claimed Depot Key and renamed it Atsena Otie Key. Cedar Key became an important port for lumber and naval stores. By 1860, two mills on Atsena Otie Key were producing cedar slats shipped to northern pencil factories. That same year, David Levy Yulee's Florida Railroad reached the islands, making Cedar Key the western terminus of a line connecting to Fernandina Beach on the Atlantic coast. The first train arrived on March 1, 1861, just weeks before the Civil War began. Confederate forces at Cedar Key scored an early naval coup: on July 3, 1861, Lieutenant Colonel M. Whit Smith led two rifle companies and a six-pounder cannon twenty miles offshore on the steamer Madison, capturing four Federal schooners and effecting the first capture of a U.S. Naval officer at sea during the war.

Congress appropriated funds for a lighthouse on Seahorse Key in 1850, and the Cedar Key Light was completed in 1854. The lantern sits atop a hill, placing the light well above sea level and visible for miles across the Gulf. Wood-frame residences were later added to each side of the structure. When war came in 1861, Confederate agents climbed the tower, extinguished the light, and removed its supply of sperm whale oil. Parsons and Hale's General Store, built on Way Key in 1859 -- the same year the town was platted -- still stands today as the Island Hotel, one of the oldest commercial buildings in the region. Together, the lighthouse and the hotel anchor a landscape where the 19th century has never fully let go.

Cedar Key's relationship with hurricanes is as old as its recorded history. The 1842 storm that ended the Seminole War military presence was only the beginning. In November 2020, Hurricane Eta made one of its Florida landfalls near Cedar Key as a tropical storm. In August 2023, Hurricane Idalia brought storm surge that reached record levels above high tide, damaging businesses along Dock Street. Then in September 2024, Hurricane Helene surpassed Idalia's record, delivering major floods, wind gusts, and a new high-water mark. Each time, the town of fewer than 700 people rebuilds. Cedar Key endures the way its namesake trees once did -- stubbornly rooted in shallow soil, bending under winds that would snap something less determined.