Iran is one of the influential countries in the Middle East and has been affected by, as well as involved in, regional political and security developments. Although Salafi thought and Salafi-jihadist movements have not posed a uniform or constant threat to Iran’s national security, the country’s religious, ethnic, and cultural diversity, together with its regional and international circumstances, make the study of the potential security implications of such movements particularly important. The main objective of this study is to analyze the direct and indirect security threats associated with Salafi and Salafi-jihadist currents in Iran, with particular attention to the eastern and western regions of the country. The study distinguishes between Deobandism as a religious and intellectual tradition and armed or jihadist organizations such as ISIS, Jundallah, and Jaish al-Adl, rather than treating them as a single ideological category. Direct threats refer primarily to violent and terrorist activities, whereas indirect threats concern the potential social and political consequences of identity-based polarization and the reduction of multiple identities to a single and exclusive identity. Drawing on Amartya Sen’s theory of Identity and Violence as its analytical framework, this study argues that the security implications of extremist currents cannot be understood solely through their violent activities; rather, attention should also be paid to the identity processes through which social differences may be transformed into exclusion, othering, and conflict. The study concludes that a comprehensive understanding of the potential security implications of Salafi and Salafi-jihadist currents requires attention to both their organizational and violent activities and the social, ideological, and identity-related contexts in which they emerge and develop.