The core of theory-driven chemistry education consists of the constant shift between the different representational domains of chemical thinking: the macroscopic, the sub-microscopic, and the symbolic domains. Because the sub-microscopic domain can neither be seen nor directly visualised, it requires specific forms of visualisation, i.e. pictures andanimations illustrating the model-based level of discrete particles, atoms, or molecular structures. This paper considers the central role visualisations play when learning about the model-based, sub-microscopic level, but it also reflects the dangers inherent in employing insufficiently examined, poorly considered, or even misleading visualisations. This is outlined using different examples taken from both textbooks for lower secondary chemistry education (for students aged 10 to 15) and from the internet. Implications for structuring and using sub-micro visualisations in chemistry education are also given.