The decline of seagrass meadows is a continuing global concern, and seed‐based restoration provides a scalable approach to recovering lost and degraded meadows. Such approaches require large quantities of seed to be collected, processed, and often stored for months until deployment. Microbial contamination during storage reduces seed viability, germination and seedling development. Losses of up to 40% of Zostera marina seeds due to contamination have been reported in northern hemisphere restoration projects, and similar issues are described here for Zostera muelleri seeds in Tasmania, Australia, highlighting the need for species‐ and region‐specific storage protocols. We conducted a 24‐week seed storage experiment using Z. muelleri seeds collected from southern Tasmania. Storage conditions included two temperatures (5 and 15 °C), crossed with four storage solutions (2.0 ppm CuSO 4 , 0.2 ppm CuSO 4 , 45 PSU seawater and ~32 PSU seawater) with and without seed surface sterilisation prior to storage. We aimed to identify conditions that suppress microbial contamination while maintaining seed viability and seedling emergence potential. Seeds stored at 5 °C in ambient seawater (~32 PSU) following surface sterilisation exhibited high survival and highest viability, with seedling emergence equivalent to that observed in hypersaline‐seawater treatments. To identify the likely causative agent of contamination, amplicon sequencing was conducted on contaminated seeds. In these samples, up to 90% of 18S amplicon reads were assigned to the fungal‐like oomycete Halophytophthora vesicula , previously identified as a seagrass seed pathogen in the northern hemisphere. We provide the first reported identification of H. vesicula as the likely contaminant of Z. muelleri seeds in the southern hemisphere and provide practical recommendations for seed storage in the presence of H. vesicula to improve seed‐based restoration outcomes.
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