Many studies have shown that active learning strategies are more effective than traditional lecture-based approaches at enhancing student understanding of challenging concepts. We have developed 30 minute, pencil-and-paper activities to test alternative hypotheses about the best way to teach experimental design, natural selection, the Hardy-Weinberg principle, phylogenetic tree analysis, and the biological impacts of climate change. Here, we present our findings for the phylogenetic tree exercise. We tested two contrasting hypotheses about the best way for students to learn the basic principles of “tree-thinking.”: either building a tree using a character matrix or analyzing an existing tree. Groups of three students in a large introductory biology course were randomly assigned one of the activities. All students completed an identical assessment the night of the activity. Controlling for student ability, we found that students in the “build your own tree” treatment performed significantly better on the assessment than students in the “analyze an existing tree” treatment. Undergraduates who had completed a modified version of the tree building activity performed equally well as first-year graduate students in a Biology PhD program who had not completed the activity. We recommend simple tree-building activities be a standard part of training for tree-thinking in introductory biology.