Modern biotechnology stands as one of the most rapidly evolving fields, with profound implications for society. This study underscores the critical importance of understanding students’ thinking in the realm of modern biotechnology. The research aims to find out the preconceptions and misconceptions held by students. Misconceptions, cognitive structures that deviate from accepted scientific knowledge, are becoming more prevalent, particularly in an era where media significantly influences younger generations. The research involved semi-structured interviews with 40 students in the Czech Republic, including 20 pupils from the final year of lower secondary school (9th grade, ages 12–14) and 20 students from the final year of upper secondary school (12th grade, ages 17–19) covering topics such as biotechnology, genetic engineering, genetically modified organisms, and cloning. The findings indicate omnipresent misconceptions, such as associating biotechnology with machinery and misunderstanding genetic engineering as genealogy. Moreover, there is a notable gap in understanding genetic engineering. The study suggests educational approaches for addressing students’ preconceptions and reconstructing misconceptions in science education. It offers a foundation for further research and the development of strategies to enhance the teaching of biotechnology and improve understanding among students and the broader public.