This study investigated students’ perceptions and comprehension of temporal aspects related to interacting with a multi-touch tabletop application called DeepTree – a dynamic visualization of phylogenetic relationships represented as a tree of life. Specifically, we explored how students engaged and used afforded zooming features of DeepTree in response to the following research questions: i) How do students interact with DeepTree in the exploration of evolutionary time? ii) How does zooming influence interpretation of evolutionary time? iii) What potential misinterpretations about evolutionary time are associated with interacting with DeepTree? Videotaped data from clinical interviews with ten secondary school students while interacting with DeepTree were analysed through a combined deductive and inductive approach. Findings show that the intensity and level of zooming interaction varied among students, and that the zooming feature was perceived in at least two ways: either as a movement in time, or as a movement in the metaphorical tree. Several misinterpretations were also observed, including the perception that zooming time in the tree corresponds to real time, that there is an implicit coherent timeline along the y-axis of the tree, and that more branch nodes correspond to a longer time. While students expressed their interactive experiences with the dynamic visualization as highly engaging, immersive and intuitive, the results suggest that DeepTree may not be optimal for comprehending all temporal aspects of evolutionary time. However, the zooming interaction provides compelling pedagogical opportunities for adapting the visualization to further develop and integrate sensorimotor and visual experiences for this purpose.