The main objective of this study was to investigate the effectiveness of animation based biology instruction for a 7th grade students’ conceptual understanding of the structure and function of flowering plant at Eweketfana primary school. The study employed Quasi experimental pre –post-test, control and experimental group design. Out of four section grade 7th students, two sections were selected randomly. The research samples comprised of 107 grade 7th students. The experimental group who were taught using animation based teaching method consisted of 55 students and the control group who were taught using traditional teaching method consisted of 52 students. Data were collected using multiple-choice tests, observation, and informal assessment. Data obtained from tests were analyzed quantitatively through mean, standard deviation, independent t-test and paired sample t-test. The observation and informal assessment data were analyzed qualitatively. The pre-test results revealed that there was no significant mean difference between the two groups. Additionally, the result of pre informal assessment showed that students in both groups had common misunderstanding about the topic. However, the post-test results imply that there was a significant mean difference between the two groups of students. Similarly, the post informal assessment comparison of the two groups, students in animation teaching method exhibited significant conceptual change compared to the traditional group of students. From the overall result of this study, it is possible to conclude that in order to improve students’ conceptual understanding and minimize their misconception about the concept of structure and function of flowering plant; it is more preferable to use the animation teaching method than traditional teaching method.