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Visual models are a necessary part of molecular biology education because submicroscopic compounds and processes cannot be directly observed. Accurately interpreting the biological information conveyed by the shapes and symbols in these visual models requires engaging visual literacy skills. For students to develop expertise in molecular biology visual literacy, they need to have structured experiences using and creating visual models, but there is little evidence to gauge how often undergraduate biology students are provided such opportunities. To investigate students’ visual literacy experiences, we surveyed 66 instructors who taught lower division undergraduate biology courses with a focus on molecular biology concepts. We collected self-reported data about the frequency with which the instructors teach with visual models and we analyzed course exams to determine how instructors incorporated visual models into their assessments. We found that most instructors reported teaching with models in their courses, yet only 16% of exam items in the sample contained a visual model. There was not a statistically significant relationship between instructors’ self-reported frequency of teaching with models and extent to which their exams contained models, signaling a potential mismatch between teaching and assessment practices. Although exam items containing models have the potential to elicit higher-order cognitive skills through model-based reasoning, we found that when instructors included visual models in their exams the majority of the items only targeted the lower-order cognitive skills of Bloom’s Taxonomy. Together, our findings highlight that despite the importance of visual models in molecular biology, students may not often have opportunities to demonstrate their understanding of these models on assessments.