The Santo Oro was acquired by Marco Pollo in his quest to find El Dorado; he needed the Santo Oro to journey to MooShu, as (apart from Marleybone's navy), only MooShu Skiffs were allowed to fly in MooShu's Skyways.
Following his journey through the Spiral in search of the wonder that is El Dorado, Marco Pollo retired from sailing; however, before leaving for Valencia to start a new life, he gave Christopher Clark- his navigator and best friend -the Santo Oro as a gift and an item to remember him by.
Unfortunately, word of the Santo Oro spread quickly. A golden ship isn't the easiest thing to make inconspicuous, so it was only natural that some people would hear of the ship and try to take it for themselves. It was Christopher's bad luck that the person who heard about it and reached him first was the dread pirate Captain Barnabus Blood. With his crew right behind him, Captain Blood easily overpowered Clark, stole the Santo Oro and took Clark's shard of the Map to El Dorado (as well as his share of the gold), leaving him poor. Blood then stashed the ship in his treasure cave in the Motherload Mine in Haunted Skyway, where it remained for quite a while.
By the events of Pirate101, the Santo Oro still sits in the treasure cave, as pristine as it was all those years ago. However, taking it was easier said than done, as Deacon had laid an ambush. Despite this, the player easily exhausts the Armada troops and dismantles Deacon. With the Santo Oro in hand, the player has (quite literally) a "golden ticket" straight to MooShu, as it is the only kind of ship allowed in MooShu (also, it has the necessary Windstone).
While in MooShu, the player uses the Santo Oro exclusively.