In this paper we describe the construction of a taxonomy for port security systems that we performed as part of the EU FP-7 project SUPPORT (Security UPgrade for Ports). The purpose of the taxonomy is to enable port stakeholders to exchange information and to provide them with computer-based automatic decision support systems, assisting the human operator in the assessment of threat levels for a number of pre-defined threats. The decision support system uses text based automatic reasoning and high-level information fusion to identify threat indicators in the input data. Thus, the existence of a taxonomy containing well-defined terms that can be used by the reasoning system is essential. In the paper we describe the method used to construct the taxonomy, viz. first constructing a draft taxonomy and then gathering feedback on this using questionnaires. The questionnaires were motivated by the necessity to embody experience and knowledge from different groups of people involved in the project, most of which are not used to formally defining their vocabulary. Over-all, the method proved to work well and produced the expected result, namely a basic taxonomy that can be used by a decision support system, and that can be extended during the project according to need.