Viewed from sea, it is easy to see why a lighthouse was needed here. With a low coast and many trees, and many oyster banks and shoals, it was important that the entrance to the river be clearly marked.

St. Marks Lighthouse is the only lighthouse in Florida with wooden stairs. The stairs are connected to a large wooden pole (it looks almost like a ship's mast) that stands in the center of the tower. Close examination of the stairs and center post shows that the stairs are attached by nails. A rope handrail was provided for use on the outside of the tower. The windows in the tower are square. They are protected with stout wooden shutters. There is a small watchroom landing at the top of the wooden stairs. From the watchroom to the lantern room, a short flight of narrow metal stairs leads up to a small metal trap door.

The actual builders were Benjamin Beal and Jairus Thayer. The superintendent of Lights for the District of Magnolia refused to accept the lighthouse as completed in March, 1830 and charged the builders with deliberate fraud against the United States Government. Arbitrators were appointed to examine the lighthouse, and the walls were found to be hollow instead of solid as called for in the contract.

The tower was rebuilt by Calvin Knowlton. The reconstruction was completed January 29, 1831. Samuel Crosby was appointed the first keeper January 18, 1830, and entered duty in the middle of February, 1830.

During the Seminole War the Samuel Crosby, the lighthouse keeper, requested a guard be established to protect the lighthouse from Indian attack. Stephen Pleasonton, General Superintendent of the Lighthouse Service, refused to approve of the guard or to comply with a request that a vessel be provided for the keeper in which he and his family might escape should the Indians attack.

The St. Marks Lighthouse was constantly battered by storms and hurricanes. In 1842 it was removed to a more secure position and a new tower was built by Calvin Knowlton. As a result of damage done by a gale on September 17, 1843, a contract for a new keeper's dwelling was made with David Carey of Fall River, Massachusetts, and a contract for a sea wall was given to Francis A. Gibbons, of Baltimore, Maryland, in 1844.

During the Civil War, the Confederates, in an attempt to blow up the lighthouse, seriously damaged the base of the tower. The work of re-establishing the light, which had been extinguished by the Confederates, was begun in September 1866, and the light was re-lighted on January 8, 1867.

The 2,000 candlepower flashing light is visible for 15 miles, shining from the top of the white conical tower, 82 feet above the water, and 80 feet above the ground. It is located on the North side of Apalachee Bay, on the east side of the entrance to the St. Marks River.