The tree of life provides a fundamental roadmap to understanding biodiversity, yet requires integration across scales of the biological hierarchy and a unique set of tree thinking skills. This combination can be challenging for undergraduates at the introductory level because of their preconceptions regarding distinct fields of biology compounded by the unique structure of phylogenetic trees. To address these two challenges while providing an undergraduate research opportunity, we developed an activity for introductory biology students that integrates molecular, organismal, and evolutionary biology. This activity relies on woody plant identification, comparative morphology, and DNA sequence analysis to teach students how to reconstruct and interpret phylogenetic trees. After building separate phylogenetic hypotheses using morphological characters and molecular data, they compare their results with a master Tree of Trees to identify instances of homology and homoplasy. After delivering this activity, the majority of students scored the activity as “helpful to very helpful” in increasing their understanding of these concepts. Overall, we deliver a framework for developing comparable Tree of Trees-type activities that leverage students' interests in familiar organisms and requires them to span scales of the biological hierarchy while improving their tree thinking skills.