Contributions of microbial communities to biogeochemical processes in oxygen minimum oceanic zones are being realized through the applications of molecular techniques. To understand seasonal and depth-wise variations in bacterial community structure (BCS) in the Arabian Sea oxygen minimum region, extensive sampling and molecular analyses were carried out. 16S rRNA gene sequencing was done to profile the BCS from five depths, surface (5 m), deep chorophyll maximum (43–50 m, DCM), 250 m, 500 m and 1000 m during Spring intermonsoon (SIM), Fall intermonsoon (FIM), and Northeast monsoon (NEM) seasons. Sequencing of 743 chimera-free clones revealed a clear vertical partitioning of BCS between the surface (surface + DCM) and OMZ (250 + 500 + 1000 m) layers. There was no distinct seasonal difference in the BCS. Most 16S rRNA gene sequences were affiliated to <i>Gammaproteobacteria</i> (39.31 %), <i>Alphaproteobacteria</i> (23.56 %) and <i>Cyanobacteria</i> (20.2 %). Higher diversity and OTUs in OMZ predominantly consisting of <i>Alteromonodales</i>, <i>Sphinogomonadales</i>, <i>Rhodobacterales</i>, <i>Burkholderales</i>, and <i>Acidimicrobiales</i> we observed might be due to their microaerophilic metabolism, ability to degrade recalcitrant substrates and assimilate sinking particulate matter. Further hitherto undescribed diversity both in surface and OMZ layers was evidenced. Implicit role of extant bacterial community in denitrification and anammox and in sulphur oxidation is highlighted.