Spatial ability predicts success in STEM (Science, Technology, Education, and Mathematics) fields, particularly chemistry. This paper reports two studies investigating the unique contribution of mental rotation ability to spatial thinking in a STEM discipline. Using authentic disciplinary tasks from chemistry, we show that the difficulty of a spatial disciplinary task varies with the spatial complexity of the stimulus and the axis of rotation regardless of the representation used in the task. We also show that spatial thinking may depend more upon students’ developing representational competence in this STEM discipline than spatial ability. These findings suggest that curriculum and assessment designers must more carefully consider how different representations are used in the STEM classroom for both learning and evaluation. We argue that educational interventions that target representational competence may be more effective at supporting spatial thinking in STEM than those that attempt to train generic spatial ability.