In many coastal areas of Japan, local fishermen manage fish and other marine resources in a sustainable manner. Such areas are referred to as "Satoumi". In this study, we focused on Hinase Junior High School in Okayama Prefecture, Japan, which is implementing a proactive marine education program in collaboration with local fishermen to maintain "Satoumi". We conducted semi-structured interviews with the students (n = 108; thirty-six students in each grade [seventh-, eighth-, and ninth-graders]) at Hinase Junior High School. Using the grounded theory, we identified students' perceptions of this program as well as of the sea. The results revealed that the program appears to have changed students' perceptions, such as recognizing the importance of the sea and eelgrass as well as their behavior such that they no longer throw waste into the sea. The higher the grade level was, the more that students felt close to and were willing to care for the sea. Our study suggests that the program has helped to develop individuals who are knowledgeable about the fishing community of Hinase, fishermen's roles, and activities that would contribute to biodiversity conservation and who are motivated to conserve "Satoumi" in the future.