Molecular biology can be challenging for undergraduate students because it requires visual literacy skills to interpret abstract representations of submicroscopic concepts, structures, and processes. The Conceptual-Reasoning-Mode framework suggests that visual literacy relies on applying conceptual knowledge to appropriately reason with the different ways of representing concepts in molecular biology. We used this framework to specifically explore visual literacy related to chromosomes. We conducted 35 semistructured interviews with students who had taken at least a year of college-level biology courses, and we asked them to sketch chromosomes, interpret an abstract representation of chromosomes, and use the abstract representation to answer a multiple choice question about meiosis. While many participants used the correct vocabulary to describe chromosome structure and function, probing their visual literacy skills revealed gaps in their understanding. Notably, 97% of participants (34 of 35) held conceptual errors related to chromosome structure and function, which were often only revealed in their sketches or explanations of their sketches. Our findings highlight the importance of scaffolding visual literacy skills into instruction by teaching with a variety of visual models and engaging students in using and interpreting the conventions of abstract representations of chromosomes.