Before Florida became a U.S. territory in 1821, this land was owned by Spain. In 1807 parcels of land to the north of the city gate were granted to residents interested in farming. However, as a defense measure, Governor Enrique White set out a specified area to guard against foreign incursions. Each grantee was allowed one small thatched palm shack but had no claim against the government in case a shack had to be burned as a military necessity. The land was granted to Jose Barrera who deeded it to Lorenzo Capella in 1819, who sold it to the Reverend Thomas Alexander.
As a result of a yellow fever epidemic in 1821, the city fathers realized that no place existed to bury non-Catholics. The Tolomato cemetery inside the city gates was barred to non-Catholics. On September 11, 1821, the city council initiated a search for a suitable lot for a "public burial place for all Protestant denominations of Christians." The city officials received permission from the United States to use half this acre as a public cemetery. A burial fee was established by the city council requiring families of the deceased to pay four dollars to the Municipal Sexton, with the city paying the expenses of the "indigent poor". The land eventually was in the custody of the Episcopal and Presbyterian congregations.
The Reverend Thomas Alexander, owner of this property, transferred the deed to the Trustees of the Presbyterian Church on January 14, 1832, where it exists to this day. The Reverend Alexander, with the agreement of the Presbyterian Trustees, merely continues the process by maintaining this site. The site would be used for all Protestants and the Presbyterian Trustees decreed an internment fee of three dollars for residents of St. Augustine and a five dollar fee for non-residents. At that time, one church collection each month was allocated to defray incidental cemetery expenses.
In July of 1884 the city passed an ordinance forbidding any further burials in both the Tolomato Cemetery and the Huguenot Cemetery.
Today, the Huguenot Cemetery is administered by volunteers of "Friends of the Huguenot Cemetery, Inc.", a non-profit, tax-exempt corporation since 1993. With the help of public donations, this historic place continues to be restored and preserved.
The name Huguenot has been associated with the cemetery since the 1830's and probably reinforced during the tourist boom at the turn of the century. How the name originated is not known, except that "Huguenot" was synonymous with "non-Catholic" to the people of St. Augustine for many years.
The name does not imply that members of the 16th century French Protestant persuasion are buried on these grounds. The association of Huguenots to St. Augustine is based on an incident in 1565 when Huguenots were slaughtered by the Spanish in a quest by both countries to claim Florida.
In the 1950's, cedar trees were planted on the grounds in memory of the French Huguenots who died here in 1565.