A court in Ecuador sentenced the crew of a Chinese ship caught fishing endangered sharks in the Galapagos marine reserve to prison terms on Sunday.

The Chinese-flagged Fu Yuan Yu Leng 999 was caught within the protected zone on August 13 with 300 tonnes of fish - including some 6,000 sharks, mostly protected species such as the hammerhead and the bigeye thresher.

The court announced on the third day of the trial against the crew that it was sentencing the ship captain to four years prison for committing an environmental crime with aggravating circumstances.

The ship's three top officers got three years prison, while the 16 other crew members were jailed for one year.

The court also ordered the crew to pay $5.9 million to the Galapagos National Park.

It's unclear if the Chinese crew will appeal the sentence.

"After the enormous indignation we felt, this will definitely compensate for the damage caused because a historic precedent has been set," park director Walter Bustos told AFP upon hearing the sentence.

The 138,000 square-kilometer reserve, a sanctuary for sharks, has been designated by UNESCO as a World Heritage site.

Some 27,000 people live on the 19 Galapagos islands, located in the Pacific some 1,000 kilometers off Ecuador's coastline.

The Galapagos is famous for its unique flora and fauna studied by Charles Darwin as he developed his theory of evolution.

"Zero tolerance for environmental crimes!" tweeted Ecuador's Environment Minister Tarcisio Granizo.

The Chinese ship has been confiscated and will be held in service to the Galapagos park, Granizo said.

Galapagos residents have been protesting what they say is a fleet of 300 Chinese fishing vessels located in international waters just outside the marine reserve.