The main focus of this study is to determine pre-service science teachers' cognitive structure about trichome and stoma through two alternative assessment techniques: metaphor and word association test. The study was conducted with 35 pre-service science teachers. Word association test given stoma and trichome as stimulant words was applied. Also they were asked to complete these sentences "Stoma is like/similar to … Because …" and "Trichome is like/similar to … Because …." The data obtained from both techniques were analysed according to the content analysis, frequency tables were prepared and divided into categories. With the help of these categories, the cognitive structures of pre-service science teachers and also misconceptions they had were revealed. Consequently, it was suggested that using metaphors in conjunction with word association test for determining of the cognitive structure of students in any subject would be complementary factor for each other's.