Extended Abstract: Introduction: Fundamentalism means at attempt to revive religious values and also confront ideologies and modern desires and secularism. The fundamentalists involve those who looking for removing existing international structure and establish new structure based on religious principles. In this regards, Islamic fundamentalism has turned to one of the serious threats in the international system during last three decades. It, not only, has endangered regional security but also challenged international security seriously. In other words, at the present, terrorism threats of radical groups are not limited only to the West of Asia, which is origin of Islamic fundamentalism, they also include other regions of the world; from Europe to the East Asia. In this regards, Al-Qaeda and ISIS are the most important terrorist actors that have significant role in development of the security concept and its dynamics. Research Aim: The research aim is to study terrorist groups of Al-Qaeda and ISIS comparatively. Accordingly, the main question of the research is that what are the similarities and differences of the Al-Qaeda and ISIS? , To understand these two groups better, the research focus locate on their differences. The findings of the research can be beneficial for domestic officials since Iran is living in neighborhood of Al-Qaeda and ISIS. Methodology: The research method is analytical – descriptive and the data gathered through library resources. With regard to the nature of these groups, the research has utilized constructivism theory which emphasis on self-other idea. Finding: Based on the research findings, the most important similarities of terrorist groups of Al-Qaeda and ISIS are origin of their ideology, apocalypse worldview, pragmatism, anti-western vision, believing in hierarchical structure in their system, pugnacity and bellicosity, anti-Shia approach, universality and applying cyberspace for operations and membership. However, meanwhile, they enjoy some critical and fundamental differences such as intellectual and geographical origin, establishing Islamic caliphate, leadership futures, quality of members, psychological and media tactics, operational priorities, financial resources, military strategy and structural differences, method of acquiring identity and eventually the way Al-Qaeda and ISIS look at women and minorities. Conclusion: This research concludes that despite of some identical similarities, Al-Qaeda and ISIS enjoy obvious differences in many aspects especially in structure, goals, functional scope, method of action or operation, quality of leaders and means. In spite it, the focal aims is almost the same i. e. violence against innocent people and killing them. Based on their ideology, “ the others” deserve to be killed. What is perceived is that Islamic fundamentalism is not going to stop or vanish. It, in return, is transforming to new form in contemporary day. On the basis of historical experiences, it is predictable that new Islamic terrorist group rise once again in the near future that even would be worse and dangerous than ISIS.