Hundreds of protected pangolins were found on a Chinese fishing vessel that ran aground last week on the Tubbataha reef, Philippine officials say.
The vessel's hold contained at least 400 boxes of the dead animals, also called scaly anteaters, officials said.
The pangolin is highly prized for its meat and scales in China, and for its supposed medicinal properties.
Twelve Chinese fishermen have been detained. In January a US navy vessel also ran aground on the same reef.
The Chinese vessel crashed into the Tubbataha reefs in the Sulu Sea, a Unesco World Heritage site, on 8 April.
"We found 400 boxes containing anteaters aboard the vessel, and we are now determining where these came from," coast guard spokesman, Lt Cdr Armand Balilo, told AFP news agency on Monday.
Pangolins sell for hundreds of dollars per kilogram in China and are protected in many Asian countries.
The 12 Chinese fishermen, currently detained on Palawan island, could be fined or jailed if they are found guilty of poaching. They also face attempted bribery charges.
More charges may be brought following the discovery of the pangolins.
The boat is the seventh Chinese fishing vessel caught in the area since 2002, according to a statement from Tubbataha Reefs National Park.
The USS Guardian also struck the reef south-east of Palawan island on 17 January.
The ship was dismantled to minimise damage to the reef and the US has apologised for the accident. Four navy officers on the minesweeper were relieved of their duties.
The Philippines and China have territorial disputes in the South China Sea, and engaged in a lengthy stand-off over the Scarborough shoal last year.
However, the Tubbataha reefs lie within Philippine territory, and are not considered a disputed area.
According to Unesco, the Tubbataha Reefs National Park is home to a great diversity of marine life. Whales, dolphins, sharks and turtles are among species found there.