Chemical identity, the idea that every substance has at least one property that makes it unique and able to be differentiated from other substances, is core to the practice of chemistry. Such practice requires using properties to classify as well as to differentiate. Learning which substance properties are productive in chemical identity thinking is not easy, however, because many features of substances compete for a learner's attention. Assessments that utilize open-ended questions can reveal ways that students use chemical identity thinking to classify and differentiate substances. On the basis of our previously published hypothetical learning progression of chemical identity, we developed a set of four open-ended questionnaires, which can be used to uncover students' chemical identity thinking. In attending to literature on the development of qualitative research instruments, as well as design-based instructional materials development frameworks, a four-phase process of development was generated that integrally considers four sets of stakeholders: students, teachers, educational researchers, and disciplinary experts. The development process is described, with attention to previously established criteria for quality in qualitative research. On the basis of stakeholder input and the development process, recommendations are offered for the use of the resulting Chemical Substance Identification (CSI) Survey in classrooms, and the instrument and sample responses are provided.