Recent science education reforms have emphasized the importance of students engaging with and reasoning from evidence to develop scientific explanations. A number of studies have created frameworks based on Toulmin’s (1958/2003) argument pattern, whereas others have developed systems for assessing the quality of students’ reasoning to support their scientific explanations. This article presents the centrepiece of this special issue, the Evidence-Based Reasoning Framework, which combines these two approaches to create an analytic tool intended as a foundation for assessing students’ ability to reason from evidence in writing and classroom discussions. The article reviews previous frameworks developed to assess students’ ability to reason scientifically and describes the elements of the Evidence-Based Reasoning Framework. It then provides an overview of the four articles in the special issue, each of which presents an application of the framework.