Members and associates of Jemaah Islamiya
 Abu Bakar Bashir | Commander | Indonesian | |
| Hambali | Operations Chief | Indonesian | Detained |
| Abdullah Sungkar | Religious Leader | Dead | |
| Azahari bin Husin | Bombmaker | Malaysian | Dead |
| Noordin Top | Senior Operative | Malaysian | |
| Lillie | Terrorist Operator | Malaysian | Detained |
| Yazid Sufaat | Malaysian | Detained | |
| Gun Gun Rusman Gunawan | Indonesian | Detained | |
| Abdullah Anshori | Indonesian | ||
| Mohamad Iqbal Aburrabman | Senior Operative | ||
| Dulmatin | Senior Operative | ||
| Zubair | Operative | Malaysian | Detained |
| Taufik Rifki | Financier | Indonesian | Detained |
| Yassin Sywal | Terrorist Operations Planner | Indonesian | |
| Mukhlis Yunos |  Filipino | ||
| Imam Samudra | Terrorist Operations Planner | Indonesian | Detained |
| Huda bin Abdul Haq | Indonesian | Detained | |
| Wan Min Wan Mat | Financier | Malaysian | |
| Parlindungan Siregar | Indonesian | ||
| Julkipli Salim Y Salamuddin | Senior Operative | ||
| Aris Munandar | Aide | Indonesian | |
| Fathur Rahman al-Ghozi | Bombmaker | Indonesian | Dead |
| Agus Dwikarna | Terrorist Operations Facilitator | Indonesian | Detained |
| Faiz bin Abu Bakar Bafana | Terrorist Operations Facilitator | ||
| Umar Patek | Operative | ||
| Abu Dujana | Operations Chief | Indonesian | Detained |
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