When the United States declared the global war against terrorism in the aftermath of the September 11, 2001 attacks, Southeast Asia was named the “second front,” next to Afghanistan. The presence of Al-Qaeda linked and inspired terrorist groups in the region, notably the Jemaah Islamiyyah (JI) and the Abu Sayyaf Group (ASG), considered Southeast Asia as one of the world’s epicenters of terrorism studies and counter terrorism operations. Since 9/11, the region has seen the implementation of various counter terrorism measures at the national, bilateral, regional and multilateral levels. These measures resulted in the arrest, neutralization and even killings of key terrorist personalities in Southeast Asia. Some were convinced to disengage from the use of political violence and leave terrorism behind. Yet, terrorist threats continue to loom large in the security agenda of Southeast Asian states as surviving elements of JI and AS are still planning to and wreaking terrorist havocs. While many leaders have been killed in battle, executed, imprisoned or convinced to leave terrorism behind, there are still younger members willing to take the place of their predecessors. This is attributed to the fact that the ideology of Al-Qaedaism that informs the actions of terrorist groups in Southeast Asia remains alive. Moreover, terrorism in Southeast Asia has long standing underlying ideological origins that require comprehensive and more nuanced counter terrorism measures.