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. 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. Our analysis shows how these ‘layers of knowledge’ and ‘historical anomalies’ have resulted in a number of counterintuitive aspects within the diagram that have successively lowered its pedagogical affordance. We claim that these counterintuitive aspects 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 students meet 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.