Malaysia has assisted in peacekeeping efforts in Mindanao, although in the past the attempt of President Ferdinand Marcos to retake eastern Sabah under the claim of the Sultanate of Sulu by forces through "Operation Merdeka" failed badly.

[2][3] Following the arrest of Nur Misuari in 2001, Malaysia Prime Minister Mahathir Mohamad said in a statement that they previously funded and supported the insurgencies in Mindanao, to fight against the Philippines, which also economically devastated the Moro people, but now have ceased doing so.

In the Philippines, the Kedatuan of Madja-as were founded by Datus from the collapsing Malay Peninsula and Sumatra centered Srivijaya Empire which extended even to Brunei (At their colony in Vijayapura at Sarawak), was a rump state of Srivijaya in the Visayas islands[9] at the Philippines, the Rajah Makatunao whom the Visayan 10 Datus of the Kedatuan of Madja-as rebelled against was said to be Rajah Tugao, leader of the Melanao nation in Sarawak.

Then the Rajahnate of Cebu, otherwise known as the Hindu nation of Sokbu (束務) in ancient Chinese records,[10] which had a Sanskrit-Tamil named capital: "Singhapala" (சிங்கப்பூர்) meaning "Lion-City" which is the same root word as Malaysia's neighbor, Singapore, was founded by a half Malay and half Tamil from Sumatra named Sri Lumay; while the founder of the Sultanate of Maguindanao (کسلطانن ماڬيندناو), Sharif Kabungsuwan, who ruled in the Philippines, was born from what is now the Malaysian state of Johor ( کسلطانن جوهر );[11][12] The Sultans and Rajahs of Malacca, Johor, Brunei, Banjar, and Sambas in what is now Malaysia and the Sultans of Sulu, Maguindanao, Lanao and Manila, as well as the Rajahs of Cebu and Butuan at the Philippines, also intermarried each other.

In 1959, shortly after, the Federation of Malaya, the predecessor state of Malaysia, became independent, the Philippines established a legation in Kuala Lumpur.

On the same year, then Philippine President Carlos P. Garcia made a state visit to Malaya where he discussed the formation of an Association of Southeast Asian Nations (ASEAN) with then Malayan Prime Minister Tunku Abdul Rahman.

[23][24][25][26] The people of the island complex that includes Malaysia, Indonesia and the Philippines are ethnically similar, with most speaking closely related Malayo-Polynesian languages.

The barter system was stopped in 2016 when Malaysia close its border prior to the persistent kidnapping of its tourists and citizens by militant groups based in the southern Philippines.

[39][40] Both countries, together with Indonesia are working together to secure Sulu Sea against piracy and extremist militant groups based in the southern Philippines such as the Abu Sayyaf.

[44] By 13 November, the Malaysian Government has donated a total of $1 million along with the sending of essential items such as food and medicines worth $310 thousand using the RMAF Charlie C-130 aircraft.

[52] Through the country RMAF A400M, food and medical supplies are being sent for the city internally-displaced residents,[53] with more humanitarian aid are being promised as the situation worsened.

[67] Albeit Martial Law was only a response to the formation of the MNLF insurgent group supported by the Malaysian government, to declare terrorism against the Philippines.

[68] The Philippine government offered numerous attempts to Malaysia to resolve the dispute through an International Court of Justice (ICJ) ruling in the United Nations,[citation needed] although recent Philippine government attempt for intervention on the Ligitan and Sipadan dispute between Malaysia and Indonesia on the basis of its claim to Sabah was rejected by the ICJ in 2002.

In the same year, the Filipino President Rodrigo Duterte announced in a live telecast that his new administration will pursue the Philippine claim on eastern Sabah through a peaceful dialogue with the Malaysian government.

[3][4][77][78] The threats were continued until today when some Filipino politicians seems supporting militants raids over Malaysia,[79][80] which threatening ties between the two countries.