Abstract Restoration of Zostera japonica is needed. Laboratory culture experiments to know the germination characteristics might be helpful for implementation of actual restoration. As a part of germination experiments, we explored suitable water temperature for long-term storage of Z. japonica seeds. This work was based on earlier reports of Zostera marina , which presumably has similar physiological properties to Z. japonica . This study consisted of two experiments: (1) preservation experiments to investigate the fate of stored Z. japonica seeds and (2) germination experiments to investigate the germination potential of the stored seeds. The results of the preservation experiments suggested that seed condition, that is, germinated, degraded, unstable, stable, etc., showed variations between the seeds stored at 4 and 23 °C. The majority of the seeds stored at 4 °C were germinated, while those at 23 °C seemed to be degraded, presumably by bacteria and mold. The germination experiments suggested high germination potential of seeds stored at 4 °C even after 302 days had elapsed. In conclusion, including previously reported results on Z. marina , low temperature was suitable for the preservation of seeds to maintain germination potential.