Seagrasses are globally distributed marine plants that represent an extremely valuable component of coastal ecosystems (Costanza et al., 1997, Beck et al., 2001, Orth et al., 2006), and their functional roles and ecological services are strongly influenced by interactions with microorganisms (Brakel et al., 2014, Brodersen et al., 2015). Analogous to other marine systems, environmental and anthropogenic stressors are likely to disturb or decouple the delicate ecological balance of these relationships (Smith et al., 2004, Cucio et al., 2016, Mejia et al., 2016). In this study, microbial communities associated with different microenvironments within the seagrass Zostera marina were characterised at four locations in New South Wales. 16S rRNA and ITS amplicon sequencing approaches were used to characterise seagrass associated bacterial, microalgal and fungal assemblages, and results were coupled to habitat feature data to determine the influence of environmental factors on microbial community structure. We observed strong heterogeneity in seagrass-associated microbial composition, suggesting that distinct microbiomes might be shaped by different abiotic and/or plant-intrinsic factors. The highest richness was estimated for upper leaf and surrounding sediment habitats, and the lowest for microenvironments of lower parts of the plant, and both differed between sites. There were, however, no significant differences in the composition of microbiomes between seagrasses from different locations, but those associated with different microenvironments within the plant differed strongly. To the best of our knowledge, this is the first time seagrass-associated members from three taxonomical groups are identified. Our results indicate that at the plant scale, specific microbial assemblages develop according to microenvironmental features, while at a regional scale there is a partial conservation of the seagrass microbiome. We evidenced that the core microbiome is very variable and shaped by multifaceted forces under a changing ocean, highlighting the importance of factors within the plant for host-microbe interactions that these substantial ecosystems rely on for survival. Our results contribute to a deeper understanding of the dynamics of the seagrass microbiome, revealing critical information for the health and maintenance of seagrass-based habitats.