In this paper we are interested in the relationship between disciplinary knowledge and its representation. We carry out a social semiotic analysis of a central tool used in astronomy—the Hertzsprung-Russell (H-R) diagram—in order to highlight its disciplinary and pedagogical affordances. By analysing the relationship between disciplinary knowledge and its representation in this way we claim that it becomes possible to identify potential barriers to student learning—instances where semiotic resources with high disciplinary affordance have low pedagogical affordance for newcomers to the discipline. The astronomy resource that we have chosen to analyse has played a pivotal role in our understanding of stellar evolution and as such it features prominently on all undergraduate astronomy programs. However, like most disciplinary-specific semiotic resources, today’s H-R diagram is the culmination of many years of work by numerous disciplinary experts. Over time, the H-R diagram has been revised and reworked by a number of different actors in order to reconcile it with developing observational and theoretical advances. As a consequence, the H-R diagram that we know today combines many layers of astronomical knowledge, whilst still retaining some rather quirky traces of its historical roots. In this paper we adopt a social semiotic lens to analyse these ‘layers of knowledge’ and ‘historical anomalies’ showing how they have resulted in a number of counterintuitive aspects within the diagram that have successively lowered its pedagogical affordance. We claim that the counterintuitive aspects we identify in our analysis give rise to potential barriers to student disciplinary learning. Using our analysis as a case study, we generalise our findings suggesting four types of barrier to understanding that are potentially at work when meeting disciplinary-specific semiotic resources for the first time. We finish the paper by making some general suggestions about the wider use of our analysis method and ways of dealing with any barriers to learning identified. In the specific case of the H-R diagram, we suggest that lecturers should explicitly tease out its disciplinary affordances by the use of ‘unpacked’ resources that have a higher pedagogical affordance.