The study investigated the common misconceptions of lower secondary school students regarding the concepts of photosynthesis and plant respiration. These are abstract concepts which are difficult to comprehend for adults let alone for lower secondary school students. Research of the students misconceptions are conducted worldwide. The researches show that many students do not even understand the fundamental concept that photosynthesis and plant respiration are related, mutually connected physiological functions. Many mistook photosynthesis for plant respiration and that respiration took place only in leaves where are special organs such as pores. They also believed that the plant produced oxygen over the entire day and that the most important source of food for plants is water with dissolved mineral substances. The research showed that Czech students have many misconceptions about photosynthesis and plant respiration. In the study, we finally go on to propose that teachers could eliminate misconceptions by graphic explanation of these concepts, correct chemical clarification of photosynthesis and respiration, and connecting integration about this processes. The study sample size consisted of 108 lower secondary school students (age 11-16 years) in the Czech Republic. The questions were designed in two parts: the first part was focused on the students knowledge, and the second part on the explanation of the answer. The data was analyzed in several ways first by the students' knowledge (correct/incorrect answers), then by their misconceptions (frequency of occurrence of misconceptions).