The purpose of this study was to identify the ways in which student teachers understand digestion and the digestive system and, subsequently, their ways of thinking, as reflected in their problem solving approaches and the justification schemes that they used to validate their claims. For this purpose, clinical interviews were conducted with 10 biology student teachers. According to the data, the student teachers possessed different levels of understanding that can be summarized into three categories: (1) naïve, in that their study method was unscientific and memorization-based, (2) fragmented, and (3) unsound. Their ways of thinking were congruent with their ways of understanding, and this was reflected in their explanations, which were constructed ad hoc and focused on simple linear relationships. In line with these ways of thinking, the justification schemes used by the student teachers were mainly external and empirical schemes, which are considered to be unsophisticated or lower-level. This study is the first study that attempts to reveal and classify student teachers' justification schemes in biology. Earlier studies on student learning processes have been conducted in mathematics. We discovered distinct patterns in the justification schemes used by student teachers, and these patterns were related to the nature of biology as a life science. At the end of the paper, we discuss our results and provide suggestions for teacher education and future research.