As rising sea levels alter coastal ecosystems, there is a pressing need to examine the effects of saltwater intrusion on coastal communities. Using 16S Illumina profiling, we characterized the communities of baldcypress tree (Taxodium distichum) root endosphere and rhizosphere soil bacteria. Our study utilized established sites along salinity and flooding gradients in the United States of Georgia, Louisiana, and South Carolina. We hypothesized that environmental variables, namely salinity and water level, as well as distance between sites would be correlated with baldcypress-associated rhizosphere and root endosphere bacterial communities. We found that geographic distance correlated with rhizosphere but not root endosphere bacterial communities, suggesting that the trees may have stabilized their endosphere communities via recruitment of a more specific suite of taxa from the surrounding soil. Mean water level, mean salinity, and the volume of woody debris were associated with both endosphere and rhizosphere bacterial communities in baldcypress trees. The density of host trees was also associated with endosphere community composition. Our study is the first to use 16S Illumina sequencing to characterize bacterial communities in baldcypress trees— a key restoration species in coastal swamp ecosystems under threat from rising sea levels.