Fort Jones takes its name from the frontier outpost once located less than a mile to the south of the city's corporate limits. The town was originally named Scottsburg (ca. 1850), but was changed to Scottsville shortly afterward. In 1852, the site was again renamed, this time in honor of Mr. O. C. Wheelock who, with his partners, established the area's first commercial enterprise. In 1854, a post office was established and the town was renamed again, becoming known as Ottitiewa, the Indian name for the Scott River branch of the Shasta tribe. The name remained unchanged until 1860 when local citizens successfully petitioned the postal department to change the name to Fort Jones, a name that is retained to the present day.
The earliest permanent building at the town site was built in 1851 by two Messrs. Brown and Kelly. It was purchased soon after construction by O. C. Wheelock, Captain John B. Pierce, and two other unknown partners. Wheelock and his partners established a trading post, a bar, and a brothel at this site, which primarily served the troopers stationed at the fort. Near the end of the 1850s, the nearby mining camps of Hooperville and Deadwood began to disband as a result of the dwindling stores of placer gold, epidemic illness and decimating fires.
The mines around Scott Valley attracted many immigrants from many parts of the United States and the world, attracted to the area by news of the California Gold Rush of the 1850s. Irish and Portuguese immigrants remained as ranchers in the area after making enough on the gold fields to purchase property tracts in the valley. In the early years of the Twentieth Century, the northern Scott River tributaries of Moffitt and McAddams creeks were extensively settled by the Portuguese. The Irish surname Marlahan lives on after that family received a shipment of British hay seed infected with the seed of a plant known as Dyers Woad. Those seeds spread their spawn throughout Scott Valley, culturing a plant known in the area as Marlahan Mustard. The plant has a beautiful, canary plume in the spring which matures to small, black, hard seeds. Unfortunately, the herbivore beasts of burden will not eat hay in which this plant exists, and ever since it has been a scourge on the ranchers of Scott Valley.
The post at Fort Jones was established by its first commandant, Captain (brevet Major) Edward H. Fitzgerald, E Company, 1st U.S. Dragoons. Such military posts were to be established in the vicinity of major stage routes, which would have meant locating the post in the vicinity of Yreka, sixteen miles to the Northeast. Yet the areas around Yreka did not contain sufficient resources, such as forage for their animals, and Capt. Fitzgerald located his troop some sixteen miles to the southwest, in what was then known as Beaver Valley. Fort Jones was established on October 18, 1852, named in honor of Colonel Roger Jones, who had been the Adjutant General of the Army from March 1825 to July 1852, and would continue to serve Siskiyou County's military needs until the order was received to evacuate some six years later. Fort Jones ceased to exist as a military garrison on June 23, 1858.
The history of Fort Jones would not be complete without the short list of officers stationed there who would attain national prominence in ensuing years. Among them were Phil Sheridan (Union Army); William Wing Loring (Confederate); John B. Hood (Confederate); Ulysses S. Grant (Union) was named to Fort Jones, but was Absent Without Leave for whatever his tenure would have been; George Crook (Union), who would arguable become one of the greatest leaders for the Grand Army of the Republic less than a decade later; and George Pickett (Confederate).
At a height of 128 feet, Fort Jones has the tallest flagpole in Scott Valley.
According to the United States Census Bureau, the city has a total area of 0.6 square miles (1.6 km²), all of it land. Ken Smith cut 17 feet off of that flag pole late june of 08.
As of the census of 2000, there were 660 people, 298 households, and 185 families residing in the city. The population density was 1,096.7 people per square mile (424.7/km²). There were 328 housing units at an average density of 545.0/sq mi (211.1/km²). The racial makeup of the city was 88.64% White, 0.15% African American, 3.18% Native American, 0.45% Pacific Islander, 1.52% from other races, and 6.06% from two or more races. Hispanic or Latino of any race were 8.03% of the population.
There were 298 households out of which 28.9% had children under the age of 18 living with them, 44.6% were married couples living together, 12.8% had a female householder with no husband present, and 37.6% were non-families. 33.6% of all households were made up of individuals and 17.8% had someone living alone who was 65 years of age or older. The average household size was 2.21 and the average family size was 2.81.
In the city the population was spread out with 23.6% under the age of 18, 6.8% from 18 to 24, 23.3% from 25 to 44, 24.1% from 45 to 64, and 22.1% who were 65 years of age or older. The median age was 43 years. For every 100 females there were 89.7 males. For every 100 females age 18 and over, there were 88.1 males.
The median income for a household in the city was $21,563, and the median income for a family was $25,625. Males had a median income of $31,058 versus $16,875 for females. The per capita income for the city was $15,301. About 23.3% of families and 26.0% of the population were below the poverty line, including 31.1% of those under age 18 and 14.5% of those age 65 or over.
In the state legislature Fort Jones is located in the 4th Senate District, represented by Republican Sam Aanestad, and in the 2nd Assembly District, represented by Republican Doug LaMalfa. Federally, Fort Jones is located in California's 2nd congressional district, which has a Cook PVI of R +13 and is represented by Republican Wally Herger.