Islamic fundamentalism as a stream of Extremist claim a return to the true Islam and no compromise with the modern world has transformed the scene inside the country and in international relations as a threat and a serious contender in today's society. In fact, after September 11, 2001, expanded a serious debate about Islamic fundamentalism around the world. But it can be difficult to provide an overview of the history of political violence in which the phenomenon of Islamic fundamentalism as its starting point after September 11, is not mentioned. However, before the date mentioned in international studies, there are also traces of fundamentalism, But what is known today as the new form of Islamic fundamentalism, since 2011 and after the rise of the Middle East, was raised around the world and to create the challenges of Political sovereignty and security for the world's most strategic regions such as Europe and then Southeast Asia (especially Indonesia and Malaysia). Therefore, this research tries to answer this question: what is the most important factor in challenging the political sovereignty of states in Southeast Asia (especially Indonesia and Malaysia). The hypothesis is Islamic fundamentalism is a rival and threat against the sovereignty and national security of Indonesia and the Philippines. The result of this study explains and demonstrates the presence and role of Islamic fundamentalism in Indonesia and Malaysia as a serious challenge in the security-political reality of these countries. Therefore, this study seeks to recognize and address the challenges and threats that are faced by these two-country with the growth of Islamic fundamentalism.
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