The purpose of the current study is to determine biology student teachers' cognitive structures on the concept of microscope. Qualitative research methodology has been applied in the study. The data were collected from biology student teachers. Free word association test and drawing-writing test were used to collect data. The data collected were subject to content analysis and divided into categories. According to the analyses conducted, while 6 categories were determined through the free word association test in biology student teachers' cognitive structures on the concept of microscope, in the drawing-writing technique, 5 categories were specified. Through both measurement tools, rich data were obtained, supporting, expanding on, and explaining one another. In this context, it was determined through both measurement tools that student teachers' cognitive structures focused on "microscope tools". Moreover, the data collected through these data collection instruments indicated that student teachers had alternative conceptions about the concept of microscope. Alternative conceptions were determined in almost all categories, which may be attributed to the fact that student teachers have naive experiences and/or the units that require the use of microscopes during the laboratory work included in biology curriculum which is provided in different teaching levels at university or pre-university education cannot be explored efficiently and appropriately.