The Fu Yuan Yu Leng 999 cargo ship was intercepted by authorities in the Galapagos archipelago marine reserve, with more than 300 tonnes of fish on board.
The huge catch included endangered species of shark, with hammerheads found butchered on the ship.
The crew, which contained roughly 20 members, could now face up to three years in prison if they are found guilty of trafficking the protected species.
It is believed the vessel is the largest ever captured inside the reserve.
Ecuador's environmental minister Tarsicio Granizo said on Tuesday that the crew were to be held in custody pending court proceedings.
He said: “Not necessarily all of the catch came from the marine reserve, but the fact that it included young sharks, even baby sharks, indicates that they could have been caught inside the reserve.”
The Galapagos' archipelago reserve is an UNESCO world heritage site protected because of the bio-diversity found there.