During the First Spanish Period (1565-1763) Florida served as a military defense port. In 1763, under British control, agricultural commerce became important. Control of Florida returned to Spain in 1783. In 1818, Andrew Jackson mounted a campaign against the Seminole Indians in North Florida that helped the United States secure Florida from Spain in 1821 and pushed the Indians south. The Second Seminole War (1835-1842) forced the Indians out of Central Florida, and the Florida Armed Occupation Act of 1842 opened the area to settlement. John Parsons, a war veteran from New Hampshire, built a large house in 1852 that became a post office and general store. He also constructed a causeway, a wharf, a custom house, and a light house. In partnership with David Levy Yulee, Parsons brought goods from Brooksville by wagon for shipment out of Bayport that were then transported by railroad from Cedar Key to Fernandina Beach. Major exports were cotton, produce, and timber. During the Civil War, Bayport exported salt and beef for Confederate troops, and was under attack by Union forces. Bayport served as the Hernando County seat from 1854 to 1856.
Post Civil War Era
Bayport had to be largely rebuilt after the Civil War. The Eberhard Faber Pencil Company of New York acquired 40 acres of land in Bayport in 1866. Cedar trees were cut and floated down the Weeki Wachee River to Bayport for shipment to Cedar Key. Bayport continued to be a major port of export until 1885, when Brooksville acquired its first railroad spur . By then, the area had been featured in nationally circulated travel guides and was a popular haven for fishermen, boaters, and sportsmen. John Parsons' home became the Bayport Hotel following his death in 1888, and for many years after 1909 was managed by Frances Goethe. She and her son Henry operated a commercial fishing operation that shipped fish from Bayport to Centralia, a nearby lumber town with a railroad spur to Brooksville. The hotel ceased operations and burned in 1942. During Prohibition, Bayport's remote location gave rise to bootlegging operations. During World War II, a radar installation was in use for bombing practice by planes from MacDill Air Force Base. A former bird rack rookery, built and used to collect dung from cormorant birds for fertilizer production, was used for target practice by the Army Air Corps.