Since the dissolution of Social Federal Republic of Yugoslavia (SFRY) in the beginning of the 1990s Bosnia and Herzegovina become independent. Montenegro was, after SFRY, federal unit in two states: Federal Republic of Yugoslavia and Serbia and Montenegro and become independent in 2006. Bosnia and Herzegovina and Montenegro are evolved from accusations of aggression to good neighbouring and security cooperation. Since Montenegro is member of NATO and Bosnia and Herzegovina is still making an effort for the membership security cooperation is necessary. Research in this paper is about security cooperation in armed forces, police and other law enforcement agencies and civil protection since both countries become independent.