<p>Benthic bacteria, in particular those existing in seagrass rhizosphere, play pivotal roles in supporting the growth and health of their hosts and also in nutrient cycling. Abundant (AT, relative abundance ≥ 0.05%) and rare (RT, relative abundance ≤ 0.001%) taxa reflect two distinct species pools in bacterial communities that differ in their structure and function and are assembled by different ecological processes. However, the mechanisms and factors controlling their spatial β-diversity patterns and ecological assembly are least understood in tropical seagrasses compared to their temperate counterparts. As rhizospheric effect vary between single and mixed plant communities, we examined AT and RT in both mono- and mixed species seagrass meadows and compared them with bulk (un-vegetated) sediments in a tropical coastal lagoon, Chilika (India). Results showed that the β-diversity (Bray–Curtis dissimilarity) of the AT and RT differed across seagrass meadows. RT exhibited a much stronger decay in community similarity with increasing spatial distance between samples than the AT. Spatial variation in RT was driven almost entirely by species turnover, whereas in AT both nestedness and turnover components played an important role. All AT were habitat generalists with broader niche breadth and environmental tolerances, while the majority of RT (66%) were specialists possessing narrower niche breadth and lower environmental tolerances. Stochastic processes (mostly dispersal limitation, 70.65–89.71%) contributed to the assembly of AT in both seagrass and bulk sediments, while deterministic factors (primarily variable selection, 45.78–60.78%) controlled the assembly of RT. Overall, this study highlighted the importance of examining AT and RT in bacterial communities for a broader understanding of the spatial patterns and underlying assembly mechanisms in tropical seagrass meadows.</p> Graphical Abstract <p></p>