Although the microbial diversity of the Indian Ocean has been extensively investigated,little is known about the community composition of microbes in the Southern Indian Ocean.In the present study,we divided 60 water column samples on the Ninety-East Ridge(NER)into five water masses according to the temperature-salinity curves.We presented,for the first time,a full description of the microbial biodiversity on NER through high-throughput amplicon sequencing approach,including bacteria,archaea,and fungi.We found that bacteria exhibited higher richness and diversity than archaea and fungi across the water masses on NER.More importantly,each water mass on NER featured distinct prokaryotic microbial communities,as indicated by the results of non-metric multidimensional scaling.In contrast,fungi were eurybathic across the water masses.Redundancy analysis results demonstrated that environmental factors might play a pivotal role in the formation and stability of prokaryotic communities in each water mass,especially that of archaea.In addition,indicator species might be used as fingerprints to identify corresponding water masses on NER.These results provide new insights into the vertical distribution,structure,and diversity of microorganisms on NER from the perspective of water mass.