Founded after Spain relinquished Florida to the United States in 1821. Micanopy became the first distinct American town founded in the new US territory. Originally an Indian trading post, Micanopy was built under the auspices of the Florida Association of New York. A leading member of the company, Moses E. Levy, along with Edward Wanton, a former Anglo-Spanish Indian trader, played important roles here. In 1822, a select group of settlers and skilled craftsmen departed New York harbor and set sail for Florida. After disembarking on the banks of the St. Johns River (at the site of present-day Palatka), and with the added labor of 15 slaves, these men forged a 45-mile road with eight bridges to Micanopy — a vital new pathway into the interior. These first settlers arrived on February 12 1823, and were in close contact with both Seminole and Miccosukee Indians, as well as black descendants of runaway slaves who resided among them. This initial period was one of relative peace. Micanopy means "head chief," a title awarded to the leader of the Alachua Seminoles. For a time, this frontier hamlet was also known informally as "Wantons."
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On the onset of the Second Seminole War in December 1835 caused great devastation. Nearby sugar plantations and homesteads were burned and entire families sought the safety of Micanopy, which had been barricaded with log pickets and renamed Fort Defiance by the military. During the summer of 1836, the Battle of Micanopy and the Battle of Wilika Pond took place here. On August 24, with most soldiers sick or wounded, the US Army evacuated the fort and town and all buildings were intentionally burned. Afterward, Fort Micanopy was erected in 1837. The town was rebuilt after the Seminole War, with few of the original inhabitants returning. Cotton replaced sugar cane as a staple crop and cattle production assumed new importance. Following the Civil War and with the advent of the railroad, the Micanopy area became known as the "leading orange and vegetable growing section of Florida." After a freeze in 1894-95, orange cultivation was curtailed, but farmers continued to flourish by growing winter vegetables for northern markets. By the 1920s, truck farming was largely displaced by the lumber and turpentine industries. Many of the town's larger surviving homes reflect the previous era of agricultural prosperity.
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