Alligator was laid down on 26 June 1820 by the Boston Navy Yard; launched on 2 November 1820; and commissioned in March 1821 – probably on the 26th – with Lieutenant Robert F. Stockton in command.

Lt. Stockton had been given command of Alligator as a result of his dogged efforts to persuade the Secretary of the Navy, Smith Thompson, to pass over several officers senior to him so that, in addition to cruising the west African coast to suppress the slave trade, he might also search for and acquire a stretch of the coast of Africa for the American Colonization Society.

Though she captured several slavers, among which were the schooners Mathilde, L'Eliza, and Daphne, perhaps her greatest contribution was the selection and acquisition of the territory around Cape Mesurado by her commanding officer and a representative of the American Colonization Society, Dr. Eli Ayers, who was embarked in Alligator for that purpose.

The negotiations with the primary native chieftain, King Peter, involved great danger since his people were noted slavers themselves.

Lookouts on the American schooner soon reported that the stranger was wearing a distress flag, and Alligator moved in to offer assistance.

However, when the warship entered gun range, the supposedly endangered vessel opened fire upon her and hoisted the Portuguese flag.

The wind was slight that day, and Alligator weathered several hours of bombardment and suffered several casualties before she had the enemy within range of her own guns.

Records of this action have identified this vessel by two slightly different names, Mariano Faliero and Marianna Flora, Stockton deemed her to be a pirate, put a prize crew on board, and sent her back to the United States to be condemned by an admiralty court.

In the short, but sharp, fight, Alligator lost her commanding officer, Lieutenant William H. Allen, wounded mortally by two musket balls.

[1] Before dawn the following morning, she ran hard aground in Hawk Channel on what is now known as Alligator Reef off the coast of Florida.