The role of microbiomes in host ecology is increasingly recognized as a potentially important force driving the ecology and dynamics of a broad range of ecosystems. However, these communities are often so complex that determining the factors (environment, dispersal, host-interactions) driving these assembled communities can be difficult. In my dissertation, I explored various factors might be driving the assembly surface microbiome of Zostera marina, eelgrass. Eelgrass is a marine angiosperm found in coastal waters across the Northern Hemisphere and provides a variety of ecosystem services including sedimentation, habitat creation and carbon sequestration. I have investigated patterns of surface communities of bacteria on both leaves that are largely surrounded by seawater and roots that grow in anoxic, highly sulfidic sediments to understand how these communities connect and modulate eelgrass’s interactions with its environment. In Chapter 1, I begin by identifying and exploring what the unique components of the eelgrass microbiome are by using artificial mimics. I deployed above and belowground mimics and found roots and leaves, but especially roots, host unique microbial communities compared to mimics. Based on differences in taxa between mimics and plant tissue, I suggest that leaf-associated microbiomes may have key roles in mediating plant-microalgal-pathogen interactions and that root-associated taxa with enhanced associations with sulfur and nitrogen cycling may ameliorate environmental stress. Furthermore, in this chapter, I identify future candidates for manipulation to further identify their specific roles on eelgrass. In Chapter 2, I examined the role of host vs. environment in structure and assembly of eelgrass microbial communities. Through a reciprocal transplant experiment, I found that even on a fine scale, microbial communities quickly resemble where they are transplanted to rather than where they are transplanted from. Additionally, I found that degree of phylogenetic community clustering varied by site suggesting environmental differences drove different community processes across these sites. Finally, in Chapter 3, I take these associations into the lab to experiment with reduced diversity environments. Through manipulations of source microbial pools via autoclaving sediments and host specific associates via bleaching root surfaces, I identify that most microbial communities are sourced from their adjacent sediments. In this reduced diversity environment in autoclaved sediments, I also identify that communities are more variable than in normal source environments and that genotype of plant has a role in determining the microbial community present. This suggests that while source and environment are critical in determining microbial community structure, there is also a role in plant-microbe feedbacks that structures assembly of host-associated microbial communities in seagrass. Through these experiments, I determine that environment plays a predominant role in the assembly of these microbial communities on both leaves and roots. I suggest that there are also smaller, but important roles of interactions with host plant and dispersal in structuring these communities. Continuing work will focus on disentangling how different plant traits influence microbial communities within different and variable environments.