This article examines how inter-governmental institutions such as regional organizations may affect cross-border cooperation. In doing so the focus of analysis becomes the wider Black Sea area where there is a parallel process of border areas cooperation and of regional, inter-governmental policy coordination, the latter led by the organization of Black Sea Economic Cooperation (BSEC). Institutionalized collaboration between sub-state actors across borders has been encouraged in the Black Sea area as a means of practical problem-solving in a broad range of fields reflecting a top-down approach. Still, regional, inter-governmental institutions such as BSEC by adhering to politics of state interest have played a limited role in providing resources for cross-border cooperation as they have been neglecting the role of non-state actors. The securitization of cross-border cooperation comes as the outcome of the seriousness of transnational organized crime harbored, destined to or transiting the Black Sea countries and the high security dilemma among the Black Sea states.