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Middleburg is rural and unincorporated area and census-designated place within Clay County, Florida, United States, located 26 miles (42 km) southwest of downtown Jacksonville and 16 miles (26 km) northwest of Green Cove Springs, the Clay County seat.

Middleburg began in the 19th century with several different names. It was first known as Clark’s Ferry from the 1820’s to 1833. The name derived from Asa Clark who ran the ferry until 1828. Fort Heilman protected settlers at Clark’s Ferry where it was the “principal depot for the east coast of Florida.During the Seminole Wars Fort Heilman was used as a quartermaster workshop and storage depot but was abandoned after the war in 1841. From 1833 to 1850 the area was then known as Gary’s Ferry after Samuel Y. Gary. On September 8, 1853 the area was finally called Middleburg. The new town traded in timber, citrus fruits and crops from farmland. When Clay county was created in 1858 Middleburg became the temporary county seat until 1874.

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