Despite a history of extremism and unconventional political developments in Kenya, relatively little empirical research has been done to determine why and how individuals join al-Shabaab and the Mombasa Republican Council (MRC). This paper is based on interviews with Kenyan and Somali-Kenyan individuals associated with al-Shabaab and the MRC. These organisations have very different profiles. Al-Shabaab pursues an Islamist terrorist agenda while the MRC pursues a secessionist agenda; the latter has not carried out terrorist attacks. Muslim youth have joined extremist groups as a counter-reaction to what they see as government-imposed 'collective punishment' driven by the misguided perception that all Somali and Kenyan-Somali nationals are potential terrorists. As long as Kenyan citizens exclusively identify with an ethnic/religious identity that is perceived to be under threat, radicalisation will increase.