Eelgrass (Zostera marina) is a marine foundation species essential for coastal ecosystem services around the northern</p><p>hemisphere. Like all macroscopic organisms, it possesses a microbiome which may play critical roles in modulating the interaction</p><p>of eelgrass with its environment. For example, its leaf surface microbiome could inhibit or attract eukaryotic epibionts which</p><p>may overgrow the eelgrass leading to reduced primary productivity and subsequent eelgrass meadow decline. We used amplicon</p><p>sequencing of the 16S and 18S rRNA genes of prokaryotes and eukaryotes to assess the leaf surface microbiome (prokaryotes) as</p><p>well as eukaryotic epibionts in- and outside lagoons on the German Baltic Sea coast. We addressed biotic and environmental drivers of microbiome community composition and diversity as well as the effect of DNA preservation and extraction bias on perceived community structure.