The Mediterranean has long been a space of encounter between different nations, religions, and cultures. The fusion of national and religious identity in the region has added complexity to current debates regarding the recognition and accommodation of religious minorities. In this introduction, we outline recent scholarship on religious nationalism and the governance of religious diversity in the Mediterranean. We draw upon the articles included in this special issue to highlight the distinctive modalities of the religion-national identity link that exist in the region, and the manner in which these modalities have influenced policies of religious accommodation and strategies of political mobilization among religious minorities. In concluding, we draw attention to the need for more studies that help to connect recent analyses of ethno-religious and political transformations in the Mediterranean with the work of historians and social scientists on the historical constitution and evolution of the region as an interconnected space in which core socio-political and cultural dynamics are shaped by cross-border flows, engagements, and exchanges.