^Clashed with JI leaders on strategy and tactics. Later pledged allegiance to ISIL.
^Irfan S. Awwas assessed the decision to disband Jemaah Islamiyah as "a belated awareness at the wrong time" and refused to disband.
^Splinter of Jamaah Ansharut Tauhid. Claims no affiliation to ISIS or JI.
^Pledged allegiance to ISIL. The organization claims it is not a terror organization, however, reports by the Indonesian National Counter Terrorism Agency stated that JAS contributed to 7 out of 142 terrorists captured in 2023.
^Platje, Wies (2001). "Dutch Sigint and the Conflict with Indonesia 1950–62". Intelligence and National Security. 16 (1): 285–312. doi:10.1080/714002840. S2CID153528325.
^Soedjati Djiwandono, Konfrontasi Revisited, p. 135.
^Ubac, Michael Lim (7 March 2013). "Aquino: I won't allow Sulu sultan to drag PH into war with Malaysia". The Philippine Daily Inquirer. Archived from the original on 24 July 2014. Retrieved 5 November 2014. President Aquino said in a statement, 'I appeal to you (Jamalul Kiram III) — we should be really clear on this – this incident is wrong. If this is wrong, why should we (the government) lend support to this? We should support what is right… which will lead us to brighter prospects; the wrong option will only bring us ruin. That's it, that's my simple message.' He also added 'Let's not forget: What they (the Jamalul Kiram III faction) are pushing for is their right as so-called heirs of the sultan of Sulu. It's not yet clear if their rights have been transferred to the Philippines. But we (the Philippines citizens and our nation) will all be affected by their conflict (with Malaysia).'
^Karlos Manlupig (17 May 2015). "MNLF denies talks with Malaysia over Sabah". Philippine Daily Inquirer. Archived from the original on 17 May 2015. Retrieved 18 May 2015. Misuari, who is hiding after the hostilities in Zamboanga in 2013, maintains his position that only the Sultanate of Sulu can pursue the negotiations for the Sabah claim. Respecting the fervent wish of the late Sultan Muhammad Jamalul Kiram III to let alone the Islamic Sultanate of Sulu and North Borneo (SSNB) to negotiate peacefully with the Muslim leaders of Malaysia to settle the controversial issue in order not to repeat the March 2013 Lahad Datu, Sabah incident, Chairman Misuari has dismissed the media reports as unfounded and without any ounce of truth involving the MNLF in any level talks. The MNLF, however, asserted that the Sabah case is a non-issue because it is the "home-base for different tribal groupings of Muslims from different regions of Southeast Asia that have enjoyed peaceful and harmonious co-existence with the Chinese and Christian populace in the area.
^Maran, Major Arm Fence D (2008). Anatomy of Separatists(PDF) (Report). Indonesian intelligence. Archived(PDF) from the original on 17 October 2011. Retrieved 22 October 2017.
^van der Bijl, Nick (2007). Confrontation, The War with Indonesia 1962–1966. Barnsley: Pen & Sword Military Press. p. 246. ISBN978-1-84415-595-8. It was an outstanding victory, and it was a victory
^Johnson, Kirk A. (2016). The longue duree: Indonesia's response to the threat of jihadist terrorism 1998-2016. Monterey, California, USA: Naval Postgraduate School. pp. 76–77. hdl:10945/49499.
