In the study of evolution in junior high school science, students are expected to understand that vertebrates have evolved while sharing ancestors. However, there has been little research on the recognition of ancestry sharing internationally. In this study, we developed a questionnaire consisting of five category questions and administered the questionnaire to lower secondary school students who had completed the study of evolution in order to clarify the relationship between the perception of ancestry sharing and other evolutionary perceptions. Statistical analysis was conducted using the responses of 1175 students, excluding those with missing values. The results revealed the following three points: 1. the recognition of shared ancestry between mammals, such as humans and chimpanzees, was strong, while the recognition of shared ancestry between mammals and reptiles and fishes was weak; 2. there was no clear relationship between the recognition of shared ancestry and the selection of a correct diagram of the evolutionary path; and 3. the incorrect evolutionary view that vertebrates evolved toward humans while sharing ancestors was formed by the students. In the future, it is expected that lessons will be developed based on the students’ perceptions and misconceptions revealed in this study.