This paper examines the chronicle of terrorism in Indonesia and the relationship between terrorism and Islamic militancy in this nation. This research focused on bombing cases from 2001 to 2012 Data was gathered through documentary research including primary and secondary resources. This research shows that after the fall of the Suharto regime in 1998, there were bomb attacks on various targets and militant extremists were able to return to Indonesia after long period of exile abroad. They started again their activities including disseminating their radical ideology, building networks and recruiting new members in Indonesia, as well as preparing for militant actions. The perpetrators of these terror attacks were mostly associated with the Islamic radical groups like Jemaah Islamiah and Majlis Mujahidin Indonesia. These two militant groups had a close relationship with Darul Islam, an organization founded during the colonial era that aimed to establish an Islamic state and to apply Syariah as a state law. In addition, both groups became a political window for al-Qaeda in Indonesia.