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The Seahorse Head was the skull of a deceased sea-horse creature that was prey to the giant Manatee that swallowed the Howler Monkey and later the screaming Narwhal. When Guybrush was successfully voted into the brotherhood of the manatee, a suspicious Bugeye placed the seahorse head on Guybriush's bed on the Screaming Narwhal as a warning to not cross the brotherhood.
After liberating both ships from inside the manatee, Guybriush can return to inside the Manatee by holding the seahorse head, making the manatee think it is one of its food and swallow him.
Later on, Gurbruysh launches the seahorse head of the cannon onto a furious De Cava and his crew, prompting the manatee that swallow his ship to swallow the ship again.