Knowledge structure is an important aspect for defining students' competency in biology learning, but how knowledge structure is influenced by the teaching process in naturalistic biology classroom settings has scarcely been empirically investigated. In this study, 49 biology lessons in the teaching unit "blood and circulatory system" in 9th grade German classrooms were videotaped and analyzed. Before the lesson, a questionnaire was administered to the students to solicit their responses about learning motivation. After the lesson, students' learning outcomes on knowledge structure were examined with the concept mapping method. The video coding used in this study focused on the knowledge linking levels during the biology lesson. Out of the 49 classes, those with the highest and those with the lowest linking levels were selected based on the coding results. In high-linking classes, interrelated facts were introduced more often in the lessons, whereas in the lessons of the low-linking classes, isolated pieces of knowledge were predominant. The results from the concept mapping task showed that the students in the high-linking classes constructed more correct relations among the concepts compared to the students in the low-linking classes. The results remained stable even after controlling for learning motivation. These findings confirm the importance of teaching interrelated facts and concepts instead of isolated facts for fostering students' knowledge structure. As a result, based on the Bavarian biology curriculum, we develop materials and programs to enable students, student teachers, and teachers to focus on interrelated facts and basic concepts instead of isolated facts in biology lessons.