During the Civil War, the Yulee Sugar Mill was operated on the Homosassa River, supplying sugar to the Confederacy. Around the same time, Citrus became the big industry in the eastern part of the county, helped along when the Florida Orange Canal and Transit Company built a canal from the groves to the Lake Panasoffkee railhead in Sumter County allowing fruit to be barged through the canal and along the Withlacoochee River. The big freeze in 1894-95 ended the citrus industry in the county just at the time that phosphate was discovered in the area and the worker population swelled until World War I terminated the flow of phosphate to European markets, the mines closed, and the population plummeted.

Citrus County was created in 1887. The Citrus County area was formerly part of a larger Hernando County. The establishment of Citrus County meant a permanent county seat needed to be named. At the time Mannfield was the county seat. As local legend has it, the matter was to be put to vote but it took several years and a midnight raid before the issue was finally settled once and for all. The battle raged with Mannfield being favored by one side and Inverness (formerly Tompkinsville) being favored by the other. 1891, by a majority vote of the county commission it was finally approved the move the county seat to Inverness but the opposition had no intention of giving up. It is widely rumored that in a midnight raid in which the courthouse and everything that had to do with County government - records, court furniture and fixtures - was "stolen" from Mannfield and moved to Inverness by horses and wagons - including Captain (W.C.) Zimmerman, the County Clerk. Many accounts recall Zimmer refused to move from his office and was picked up with his chair and desk and transported in a wagon to the new County Seat in Inverness.

Citrus County originally was named for the county's citrus trees. Citrus production declined dramatically after the "Big Freeze" of 1894-1895. Today, citrus is grown on one large grove, Bellamy Grove. Phosphate mining also played a major part in the history of the County until the end of WWII in which phosphate mining was largely moved overseas. The first newspaper of Citrus County was called the Phosphate Times.