Difficulties in the understanding of photosynthesis by Israeli junior high school students were examined. Thirty‐three students were interviewed and asked about chemical and ecological issues of photosynthesis. Difficulties were found in their understanding of the living body as a chemical substance, lack of knowledge about the chemical elements that compose the living body, and difficulties in understanding that gas (CO2) is the source of the plant’s body. A major problem was the perception of photosynthesis as a type of respiration. Difficulties were also found in students’ understanding of concepts related to the ecosystem, such as the oxygen cycle in nature and autotrophic feeding as the first step of the food chain. Considering these difficulties, we recommend changing the way of teaching these issues. Such a programme is now being tested.