Critical thinking is one of the most important sets of cognitive abilities and dispositions required for both scientists and global citizens. In this explorative study, we examine which critical thinking aspects are perceived as relevant by biology graduate students and in what ways they found these aspects important for their scientific work. Data was collected from two cohorts of students participating in an online academic course focusing on the foundations of critical thinking. The course included weekly sessions in which different critical thinking topics were presented and discussed, followed by a seminar, in which individual students presented, reflected on, and received feedback on their biology research projects. Based on students' responses and artefacts collected during the course, several critical thinking aspects were identified as most relevant for students' scientific work, such as confirmation bias, methodological issues, and socio-cultural influences. Students also mentioned the value of open communication with peers when engaging in critical thinking. It is suggested that biology graduate students should have opportunities to learn about and engage with relevant aspects of critical thinking and to collaboratively reflect on their research using these aspects.