The research described in this paper focuses on identification of the most important indicators for emerging mycotoxins, starting from those produced by Fusarium fungi, in wheat-based feed and food supply chains, as well as the development of a conceptual model to predict the occurrence of these emerging toxins, based on the selected indicators. The selection of the most important indicators was based on a literature review and evaluation of the resulting indicators for their relevance. Each indicator selected was appointed to relevant stage(s) of the supply chain to which it is related and, for each indicator, a suggestion for a potential information source is given. The selected indicators cover various influential sectors, amongst others, weather conditions, agronomical practices, trade and legislation, as well as a variety of information sources, e.g. on-farm records and statistical organisations. The conceptual model developed is aimed at predicting the occurrence of emerging mycotoxins – based on the selected indicators – in a particular unit of wheat. The model takes a supply chain approach and can handle various types of indicators and various levels of detail of information on origin of the unit of wheat. The proposed model could be useful in the development of an identification system for emerging risks related to mycotoxins in wheat-based supply chains. Ultimately, such a system will help industry and policy makers in their decision-making process with regard to prevention and control of upcoming risks.