The 12-day amphibious landing exercises -- involving about 3,500 US marines and sailors and 1,200 Filipino counterparts -- were officially launched from the western island of Palawan, directly facing the South China Sea.
China claims the sea almost in its entirety, and its increasingly assertive efforts to stake its claims have heightened tensions with neighbours including the Philippines, which has conflicting claims to parts of these waters.
But Philippine marine spokesman Lieutenant Jerber Anthony Belonio stressed that the location of the opening ceremonies was not linked to the territorial dispute.
The Philippines has recently been beefing up its military assets in Palawan, the country's main outpost to the South China Sea which is a vital sealane, a valuable fishing ground and which is believed to hold vast mineral resources.
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The poorly-equipped military has also recently been boosting its ties with defence allies -- particularly the United States, its former colonial power -- in the face of Chinese sabre-rattling.
The US Marine Corps said the exercises would "enhance the interoperability between US Navy and Marine Corps forces and their Philippine counterparts with a focus on improving our bilateral response to regional issues and maritime security crises".
The USS Peleliu, a US amphibious assault ship, along with two support ships, arrived at the former US Subic naval base on the weekend to take part in the exercises.
In April, the two allies signed a new defence accord giving US forces greater access to Filipino bases as part of a US rebalancing of military power towards rising Asia, which is seen by many analysts as a check to the emerging power of China.
Although the United States has taken no side in the territorial disputes, it has warned China against taking "destabilising actions" in the South China Sea.