The main purpose of the study was to investigate pre-service teachers' perceptions of the criteria used to classify animals. In this regard, it was also aimed at exploring conceptual structures and reasoning patterns shaping the pre-service teachers' perceptions. The participants of the present study were 324 pre-service teachers attending science education and biology education departments in Turkey. With the aim of gaining insight into pre-service teachers' perceptions of animal classification, qualitative research method was followed in which the participants were interviewed. In addition to qualitative data, quantitative data were also collected by classification forms and in this way it was aimed to bring variety to analysis results and reinforce them. As a result of the study, the conceptual structures shaping the pre-service teachers' perceptions leading to their evaluations are subsumed under the categories of "morphological, anatomic and physiologic characteristics", "behaviour", "habitat" and "systematic". In light of the findings of the current study, it can be argued that some characteristics of animals were given greater priority while classifying them and this leads to development of some erroneous information and alternative conceptions. More holistic evaluation of the characteristics of animals may allow the development of a better perception of animal classification.