This study reported herein aimed to reveal prospective teachers' misconceptions about classification of plants and the effect of pre-service education program on their correct conceptions of this biological issue. Prospective teachers majoring in Elementary School Classroom Teacher Education constituted the target population of this study during the fall semester of the 2012-2013 academic years from Turkey. In order to reveal the difference between the misconceptions of prospective teachers who are at the beginning and at the end of their university education, the research was conducted as a cross-sectional study (78 first and 84 fourth class). The results showed that the prospective teachers in both groups have misconceptions and considerable confusion over the concepts of without-seed plants, seedy plants, vascular plants, non-vascular plants, gymnosperm plants, angiosperm plants, fruit and vegetable. In addition, the pre-service education did not seem to have an important effect on correction of prospective teachers' misconceptions about classification of plants. In this context, prospective teachers are graduated with misconceptions about classification of plants.