Most biology undergraduates learn about mutations in multiple classrooms throughout their college career. Understanding personalised genome test results, genome editing controversies, and the appearance of new variants of viruses or antibiotic resistant bacteria all require foundational knowledge about mutations. However, the abstract nature of molecular processes surrounding mutations makes them one of the more difficult topics for students to understand and apply. Instructors need valid assessment tools to document student understanding and tailor their instructional methods to address student knowledge gaps. We describe here the development and validation of the Mutations Criterion Referenced Assessment (MuCRA). This formative assessment was developed through an iterative process involving expert feedback and student responses to both open-ended and multiple-choice questions. The final MuCRA is composed of 10 multiple-choice questions aligned with three learning objectives. The item difficulty for each question was between 0.32-0.65, while the discrimination index ranged from 0.31-0.75 and the reliability (KR20) for the MuCRA was 0.69. The congruence analyses demonstrated distractors are capturing student misconceptions in 9/10 questions. These data indicate that the MuCRA can be used to reliably assess student learning and common misconceptions about mutations.