The ship is massive, as even the giantHajrudin is dwarfed by its size. The ship has three masts and its figurehead is a woman looking upwards with angel wings and a helmet based on the design of Ancient Greek helmets.
The ship was docked at the eastern port in Dressrosa when the Straw Hats and their allies from Dressrosa were fleeing the Marines. It was then sailed out to sea as the leader of the fleet of pirate ships. It came under attack by an alliance set out to kill Luffy, but the attack was disrupted by rubble falling on the attackers, and none of the rubble hit the Yonta Maria due to Fujitora protecting the ships of the Straw Hat Grand Fleet.
The ship is based on the Santa Maria, the main ship of Orlumbus' namesake Christopher Columbus on his first voyage. It is also a pun, as "San" in Santa Maria means three in Japanese, and "Yon" in Yonta Maria means four, indicating it is of a higher order than the Grand Fleet's Santa Maria and Nita Maria (three and two).
The figurehead resembles the ancient Greek goddess Athena.