Florida State University established its first marine laboratory, the Oceanographic Institute, in 1949, on 25 acres on the harbor side of the peninsula that forms Alligator Harbor, about 45 miles south of Tallahassee. The Oceanographic Institute maintained a substantial research effort throughout the 1950s and 1960s. The research conducted by the faculty and graduate students was intended to be interdisciplinary, balancing fundamental investigations of the productivity of tropical continental-shelf waters in the northeastern Gulf of Mexico with applied research on practical problems of the commercial and sport fisheries and the use of other marine resources.

Other marine stations maintained by Florida State University until 1954 included one at Mayport, on the St. Johns River near Jacksonville, which conducted research related to the menhaden and shrimp fisheries and oceanographic problems of the Gulf Stream and the mouth of the St. John's River, and one on Mullet Key at the mouth of Tampa Bay, which studied red tide.

In 1966 FSU formed the Department of Oceanography on campus, and the Oceanographic Institute was closed. A new facility was built across the harbor and further to the west on land donated to Florida State University by Ed Ball, President of the St. Joe Paper Company. This facility was known as the Edward Ball Marine Laboratory, or more recently, The FSU Coastal and Marine Laboratory.