Focusing on the resilience and vulnerability dimension of pesantren against radicalism was studied from three aspects: social bonding (identity and internal bonding), social bridging (horizontal linkage and relationship with other communities) and social linking (vertical linkage and relationship with authorities). The study was conducted from July 2019 to January 2020. Using the quantitative (questionnaire) and qualitative method (interview), the study managed to gather the data from two-hundred seven (207) persons – 161 male informants or 78% and 46 female informants or 22%, from forty-two (42) pesantrens in eight (8) provinces in Indonesia. Being categorized into three (3) main types of pesantren (traditional, modernist and salafi) and later specified into seven (7) sub types of pesantren (traditionalist, Gontor, Muhammadiyah, Persis, salafi purist, salafi tanzimi, salafi haraki), the study finds that each group has their own resilient capital as well as vulnerable loophole. For example, traditionalist pesantren has “yellow literature” (Kitab Kuning, which refers to traditional literature developed by local ulema and is considered as having more contextualized and moderate teaching) as a factor to contribute to resilience, but it has a strained relationship with other Muslim groups as a factor to contribute to vulnerability. Salafi purist’s concept of bughat that considers those not in line or even in enmity toward the authorized ruler/government as rebellious and thus is prohibited, becomes a factor to contribute to resilience, but it lacks civic value teaching as a factor to contribute to vulnerability. Nevertheless, in general traditionalist pesantren is considered as the most resilient, and then Gontor, Muhammadiyah, Persis, salafi purist, salafi tanzimi, and salafi haraki as the most vulnerable.