- AFK German Association for Peace and Conflict Studies (Arbeitsgemeinschaft für Friedens- und Konfliktforschung)
- AFP Armed Forces of the Philippines
- AKP Ansar Khilafa Philippines
- ARMM Autonomous Region in Muslim Mindanao
- ASEAN Association of Southeast Asian Nations
- Banser Barisan Ansor Serbaguna Nahdlatul Ulama (Multipurpose Ansor Front)
- BBL Bangsamoro Basic Law
- BBM Bugi, Buton, and Makassarese
- BCC Basic Christian Communities
- BIFF Bangsamoro Islamic Freedom Fighters
- BOL Bangsamoro Organic Law
- BPS Badan Pusat Statistik (Indonesian Central Bureau of Statistics)
- Brimob Brigade Mobil (Mobile Brigades)
- BTI Bertelsmann Transformation Index
- BUC Bishops Ulama Conference
- CAB Comprehensive Agreement on the Bangsamoro
- CAFGU Civilian Armed Forces Geographical Units
- CAS Comparative Area Studies
- CBA Church-based activities
- CBCP Catholic Bishops Conference of the Philippines
- CCDA Crisis Center of the Diocese of Amboina
- CIA Central Intelligence Agency
- CSIS Center for Strategic and International Studies
- DDII Dewan Da’wah Islamiyah Indonesia (Indonesian Islamic Dawah Council)
- DEPAdev Democratic Party Development
- ECID Episcopal Commission of Interreligious Dialogue
- ELALEM Maluku Interfaith Institution for Humanitarian Action
- EQMCC Enhanced Quine McCluskey Algorithm
- FAB Framework Agreement on the Bangsamoro
- FKAWJ Forum Komunikasi Ahlus Sunna Wal Jamaah (Communication Forum of the Followers of the Sunnah and the Community of the Prophet)
- FKM Front Kedaulatan Maluku (Moluccas Sovereignty Front)
- FKUB Religious Harmony Community Forum
- FPI Front Pembela Islam (Front of the Defenders of Islam)
- Golkar Partai Golongan Karya (Party of the Functional Groups)
- GPM Gereja Protestan Maluku (Protestant Church of the Moluccas)
- GRP Government of the Republic of the Philippines
- IAG Institute for Autonomy and Governance
- ICG International Crisis Group
- ICMI Cendikiawan Muslim Se-Indonesia (Association of Muslim Intellectuals)
- IMC Immaculate Conception Parish
- IS Islamic State
- JICA Japanese International Cooperation Agency
- JIM Justice for Islamic Movement
- JMA Jamaah Mohajirin Wal Ansar
- KAS Konrad Adenauer Stiftung
- KISDI Komite Indonesia untuk Solidaritas Dunia Islam (Indonesian Committee for Solidarity with Global Islam)
- KNIL Koninklijk Nederlands Indisch Leger (Royal Netherlands East Indies Army)
- Kopassus Komando Pasukan Khusus (Special Forces Command)
- Kostrad Komando Strategis Angkatan Darat (Army Strategic Command)
- LJ Laskar Jihad (Warriors of Jihad)
- LSM Living Standard Measure
- MILF Moro Islamic Liberation Front
- MIM Mindanao Independence Movement
- MNLF Moro National Liberation Front
- MOA-AD Memorandum of Agreement – Ancestral Domain
- MP Member of Parliament
- MPR Majelis Perusyawaratan Raykat
- MUI Majelis Ulema Indonesia (Council of Indonesian Ulamas)
- NASSA National Secretariat for Social Action
- NGO Non-Governmental Organization
- NKRI Negeri Kesatuan Republik Indonesia (Unitary Nation of the Republic of Indonesia)
- NPA New People's Army
- NU Nahdlatul Ulama (Ulama's Revival)
- OIC Organization of the Islamic Conference
- OLS Ordinary Least Square
- PAN Partai Amanat Nasional (National Mandate Party)
- PBB Partai Bulan Bintang (Crescent Star Party)
- PBS Partai Kebangkitan Bangsa (National Awakening Party)
- PDI-P Partai Demokrasi Indonesia Perjuangan (Indonesian Democratic Party of Struggle)"
- Philconsa Philippine Constitutional Association
- PIME Pontifical Institute for Foreign Missions
- PKS Partai Keadilan Sejahtera (Prosperous Justice Party)
- PNP Philippine National Police
- PODES Potensi Desa (Indonesian Household Survey Data)
- PPIM Pusat Penkajian Islam dan Masyarakat (Center for Islamic and Society Studies)
- PPP Partai Persatuan Pembangunan (United Development Party)
- QCA Qualitative Comparative Analysis
- RMS Republik Maluku Selatan (Republic of the South Moluccas)
- SAF Singapore Armed Forces
- SARA Ethnicity, religion, race and social relations (Suku, Agama, Ras and Antargolongan)
- SPCPD Southern Philippines Council for Peace and Development
- SPMM Suara Peijuangan Muslim Maluku (Voice of the Struggle of Moluccan Muslims)
- SWS Social Weather Stations
- TNI Tentara Nasional Indonesia (Armed Forces of Indonesia)
- US United States
- UIN Universitas Islam Negeri (State Islamic University)
- UN United Nations
- UNDP United Nations Development Program
- UNICEF United Nations International Children's Emergency Fund
- USIP United States Institute of Peace