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Captain Morgan Duck was (presumably) an anthropomorphic duck.
A notorious pirate based on the island of Drakehete (then Duckhaiti), Morgan Duck was the typical buccaneer, complete with an extravagant feathered hat, a ship with black sails, a skull-and-crossbones flags, and a hook for a hand. Morgan once stole a load of treasure from his rivals, the Coast Brothers, which he concealed within the figurehead of his ship; a parchment stating this was the treasure's hideout was then hidden in a labyrinthine cave on Drakehete proper, so that the treasure would not be forever lost in the event of Morgan's death. At some later point, Morgan was presumably killed, as his ship was dismantled, with miscellaneous objects found aboard (including the figurehead) eventually finding their way to the Drakehete History Museum.
Behind the scenes
Morgan Duck was only ever mentioned in The Beagle Boys and the Last Pirate.
Despite the similar name and professions, Morgan Duck is unrelated to Morgan McDuck. Both are simply named as an allusion to the famed Pirate Morgan (who also has a direct counterpart in the Disney comics universe, it must be said).
It is unknown if Morgan was any relation to Donald Duck's Duck family, though this seems likely.