The limits of scientific knowledge are an emerging problem in the debates about technological risk. In an exemplary analysis of the controversy surrounding genetically modified organisms (GMO), we show that the epistemic settings of two involved scientific disciplines – molecular biology and ecology – entail different types of non-knowledge and deal with non-knowledge differently. Both of these "scientific cultures of non-knowledge" are analysed along five criteria: the way of dealing with unforeseen events, the way of dealing with complexity and uncertainty, the temporal and spatial scales of knowledge, the de-and re-contextualisation of knowledge, and the epistemic (self-)reflexivity. The scientific culture of non-knowledge in molecular biology can be described as control-oriented, while that of ecology can be described as uncertainty-oriented. This difference is mirrored in the societal discourses and regulations concerning GMO. A greater variety of cultures of non-knowledge seems likely, which calls for further analysis.