A phylogeny depicts the hypothesized evolutionary relationships among taxa as a nested hierarchical branching diagram. Interpreting the relationships among taxa on a phylogeny is part of a set of skills called tree-thinking. Because published phylogenies are not constructed for the purpose of tree-thinking pedagogy, the information can be difficult for students to interpret and explicit instruction is required for mastery of the tree-thinking skill-set. We present a process to construct customizable assessment questions using published phylogenies, to assess a key tree-thinking skill, determining relatedness among taxa on a phylogeny. We detail how to construct two types of forced-choice questions: binary-choice and four-choice. In both question types, students are presented with a phylogeny and are instructed to determine which taxon from a list of taxa is most closely related to a focal taxon. The list of taxa includes distracters as possible responses explicitly selected based on common alternative strategies (similarity, proximity, node counting), in addition to the correct response. Instructors can select taxa of their own choosing in order to customize assessments. These assessment questions can be utilized during instruction as a formative assessment to enhance learning or in a summative assessment.