Belowground microbial communities have a substantial role in seagrass health and performance. These communities, and their role in seagrass performance, could vary depending on background environmental conditions at local and larger spatial scales (e.g., with latitude). We sampled rhizosphere and bulk sediment bacterial communities of the seagrass Zostera muelleri at 14 sites located in five locations across a latitudinal gradient (~ 24◦ of latitude, 2600 km). We also investigated whether variation in these communities was best explained by variation in morphological and environmental variables at the site and location scale. Rhizosphere and bulk sediment bacterial communities differed from each other at the site scale as well as between sites and locations. Notably, variation in both these communities was best explained by latitude followed by longest leaf length and belowground biomass. These insights into how seagrass belowground bacterial communities are structured provide strong evidence that their role in seagrass performance and stress amelioration vary depending on environmental context.