Cedar Key is a small city built on an island archipelago off the Gulf Coast of Florida. It's a rare gulf-water port with long stretches of tidal marsh running north and south for miles. In the early days of European colonisation, the island was covered with a dense growth of Eastern Red Cedar, hence the name. Arrowheads and spear points found in the area indicate that Paleo and Native Americans were here as long as 12,000 years ago. Nearby is Shell Mound, an ancient mound of shells, bones, artifacts and household refuse built up over maybe 3,500 years by Native Americans of the Paleo and Eastern Woodland cultures.

William Augustus Bowles built a watchtower on the island in 1801 but the Spanish found it and destroyed it in 1802. The first permanent settlement on the island began in 1839 when soldiers under General Zachary Taylor built "Fort No. 4" on Depot Key (now known as Atsena Otie Key) during the Second Seminole War. This lasted until a major hurricane in 1842 hit the area and a 27-foot storm surge destroyed virtually everything built on the islands. Later that year, the islands were opened up to settlers under the Homestead Act. The Collector of Customs of Tampa Bay filed homestead papers on the main island (and renamed it Atsena Otie Key), then bought what was left of the military buildings and spent the next several years turning the island into a major Gulf port.

In 1850, Congress appropriated the money to build a lighthouse on nearby Seahorse Key and that was lit in 1854. By 1860, there were two mills on Atsena Otie Key producing and shipping slats of cedar to pencil factories up north. The Florida Railroad arrived at Cedar Key in 1860 (actually, the depot was built on Way Key, an island you cross on the journey to Atsena Otie Key now). The still-surviving Island Hotel was built in 1859 as Parson's and Hale's General Store. The first train finally pulled into town on March 1, 1861, just before the opening volleys of the Civil War were fired.

Cedar Key saw a lot of action during the Civil War with several back-and-forth occupations on the island archipelago. The Union finally moved in permanently in early 1864 and conducted campaigns up and down the Gulf Coast of Florida from there.

After the war ended, Eagle Pencil and Eberhard Faber built pencil factories on Way Key. The railroad had sustained severe damage during the war and rail traffic didn't resume again until 1868. The "Town of Cedar Keys" was incorporated in 1869 with a population of almost 400.

Cedar Key grew steadily until 1886, when Henry Plant finished his railroad into Tampa. That started to take some of the shipping business out of Cedar Key. Then a Category 3 hurricane hit at the end of September, 1896, killing more than 100 people and wiping out most of the remaining businesses. Much of what wasn't destroyed by the hurricane burned in a massive fire in early December 1896. That sent all the shipping and most of the manufacturing to Tampa.

Folks were slow to rebuild, partly because the only industries left was fishing, sponge-collecting and oystering. Then the oyster beds became exhausted. Cedar Keys National Wildlife Refuge was established on three islands in the archipelago in 1929. The lighthouse was abandoned in 1952. Around that time, tourism started to pick up until today, tourism is probably the single biggest economic driver in the area, with clam-based aquaculture running a very close second.

Today, most of Cedar Key and environs is listed on the National Register of Historic Places as the Cedar Keys Historic and Archaeological District. It seems that every few years, the area is under the gun from one or another major hurricane but that hasn't stopped folks from building some pretty nice vacation homes on the islands. The old lighthouse is now used as a marine biology research center by the University of Florida. The Cedar Key Museum State Park offers displays of the town's 19th century history along with many samples from Saint Clair Whitman's collection of seashells and Native American artifacts.

Between 2000 and 2010, the population of Cedar Key dropped by more than 11%.