The Philippines is located in the Southeast Asian region and the country is geographically an archipelagic country with hundreds of islands of various sizes around it. Today, the Philippines is classified as a developing country within Southeast Asia. In the rapidly growing development, the Philippine government is still facing a problem where there is a prolonged political situation that involves Manila and separatis in the Southern Region. From a historical point of view, the political conflict between the Philippine government and Muslim Mindanao has long been evident even before Bangsamoro was physically colonized by the Philippine. Meanwhile, for Bangsamoro, this conflict is seen as a ancestral struggle for more than four decades. Almost every day, the news about the South Philippine is reported and broadcast by local and international media. It thus proves that conflict is still happening and getting worse so so that jeopardize the security of the surrounding community. In this regard, the Philippine Government must act wisely in order to resolve the political conflict before it becomes critical. At the same time, to be more careful when dealing with the conflict to prevent ones to take advantage of the weaknesses. In addition, various events and stories were recorded as a process for resolving conflicts this century despite the conflict still inexorable, but the development of the peace process led by Malaysia is still to be the cornerstone towards peace in the turbulent territories. Malaysia has to face some short-term and long-term impacts due to this ongoing conflict. Either directly or indirectly it will have generate the implications towards politic, economy, social and security especially in the East Coast of Sabah. This is due to several reasons, especially its geographical position factor that is too close to East Malaysia (east coast of Sabah) as well as the demographic factors of the local population in Sabah itself. Hence, any developments occurring in the southern Philippines will continue to have security implications on a small or large scale against Malaysia. Critical developments on Malaysia’s security and sovereignty peaked on 12 Feb 13, when a intruder from 100 to 200 armed men introduced themselves as the Royal Army of the Sulu Sultanate invaded Lahad Datu, Sabah. Jamalul Kiram III (Sultan) and Nur Misuari are demanding, claiming Sabah for claiming Sabah is the land of hereditary heritage of Sulu Sultanate. The intruder group is headed by Agbimuddin Kiram (King of the Young) who is one of the three heirs of Kiram Group. The intrusion in Kg Tanduo, Lahad Datu on 12 Feb 13 led Malaysian government taking an integrated action to counter the intruder’s attack on March 5, 2013.