In response to STEM education reform efforts, many instructors have incorporated active learning into their courses. However, the relationship between instructor justification to students about the use of active learning and student perception of why instructors use active learning is largely unknown. To investigate instructor active learning justifications in Introductory Biology at a large public university, we conducted class observations, syllabi analyses, and instructor surveys. Students were surveyed about their instructor's justification about the use of active learning and their instructor's motivations for using specific types of active learning. We found that instructors varied in their active learning justifications. Students were more likely to remember instructor justifications from the first day of class if the instructor justified active learning use in general rather than justifying only individual active learning types. Regardless of justification type, many students did not recall any instructor explanation. Students most often remembered their instructors saying that active learning keeps students engaged and helps students learn. However, many students had misconceptions that instructors used active learning to monitor attendance and/or give "easy" points. Clarity in active learning justification is important, but students also appear to infer instructor motivations on the basis of their active learning experiences in class.