All that remains of the city is the cemetery; the last known burial was in 1883 James French a C.S.A privatethat was born in Magnolia town in 1843.

In June 1827, only 6 years after Spain ceded Florida to the United States, four brothers from Maine, John, George, Nathaniel and Weld Hamlin founded the town of Magnolia on the St. Marks river just north of the existing town of St. Marks.

Such items of record include brown and loaf sugar, Canary, Málaga and Bordeaux wine (known then as Claret wine), bleached osnaburg, powder, shot, lead, cordage, leans soup, foolscap sealing wax and Scotch snuff.

Magnolia, St. Marks, and sister river port town Port Leon, thrived from the commerce from Tallahassee merchants and cotton plantations of the Red Hills Region of north Florida and south Georgia when their products were hauled south to Tallahassee and beyond.

There was another town named Magnolia that existed around the time of the American Civil War in Clay County, Florida, on the west bank of the St. Johns River.

Period maps place this town just north of present-day Green Cove Springs, Florida.