Evolution is at the center of the biological sciences and is therefore a required topic for virtually every college biology student. Over the past year, the authors have been building a new simulation software package called EvoBeaker to teach college-level evolutionary biology through simulated experiments. They have built both micro and macroevolutionary laboratories into the program. For labs dealing with microevolution, they were able to examine the literature to identify the misconceptions that were most prevalent among college students, and therefore most important for them to address. They could find no similar literature on misconceptions about macroevolution. They thus began their software design phase by seeking to identify misconceptions among college students about the subject of evolutionary trees, the diagrams used to display branching evolutionary relationships between populations or species (which include cladograms and other diagrams showing reconstructions of evolutionary history), and the ideas embedded in these diagrams. In this article, the authors report the most common misconceptions among college students in their understanding of evolutionary trees, and their demonstrated ability to perform typical "tree-thinking" skills. (Contains 4 figures and 2 tables.)