This article analyses current trends in and future expectations of nanotechnology and other key enabling technologies for security as well as dual use nanotechnology from the perspective of the ethical Just War Theory (JWT), interpreted as an instrument to increase the threshold for using armed force for solving conflicts. The aim is to investigate the relevance of the JWT to the ethical governance of research. The analysis gives rise to the following results. From the perspective of the JWT, military research should be evaluated with different criteria than research for civil or civil security applications. From a technological perspective, the boundaries between technologies for civil and military applications are fuzzy. Therefore the JWT offers theoretical grounds for making clear distinctions between research for military, civil security and other applications that are not obvious from a purely technological perspective. Different actors bear responsibility for development of the technology than for resorting to armed force for solving conflicts or for use of weapons and military technologies in combat. Different criteria should be used for moral judgment of decisions made by each type of actor in each context. In addition to evaluation of potential consequences of future use of the weapons or military technologies under development, the JWT also prescribes ethical evaluation of the inherent intent and other foreseeable consequences of the development itself of new military technologies.