Phylogenetic trees are a common visual representation in biology, and the most important visual representation used in evolutionary biology. Thus, phylogenetic trees have also become an important component of biology education. We sought to determine what forms of reasoning are utilized by introductory biology students to interpret taxa relatedness on phylogenetic trees, what percentage of students correctly interpret taxa relatedness, and how these results alter in response to instruction and over time. Our students demonstrated a tendency for counting synapomorphies and nodes, rather than more common misinterpretations found in current literature. Students also struggled mightily with correctly interpreting phylogenetic trees, including many who exhibited memorization of correct reasoning. Broad initial instruction achieved little for phylogenetic tree understanding. More targeted instruction on evolutionary relationships improved understanding, but to a still unacceptable level. It appears these visual representations, which can directly affect student understanding of evolution, represent a formidable challenge for instructors.