This paper presents the study on the nature of the hybrid threats and vulnerabilities of the South Eastern European region with proposals for countering these types of threats in cyberspace. The research starts with the concept of command and control warfare to understand better the doctrine of the hybrid warfare of the Russian Federation, considered as a main threat for the region. Response from NATO and EU is analyzed to identify the specific measures to be used in Southeastern Europe. Academic support in countering hybrid threats in this region is proposed as a Basic Environment for Simulation and Training (BEST) – Resilience as a first step to develop a dedicated Center of Excellence (CoE) in this domain for South Eastern Europe.