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Deep sea is an extreme environment which harbours diverse microbial communities. The deep sea ecosystem of the northeastern part of Indian Ocean is poorly studied. In this study, to explore the bacterial diversity of the unexplored environment, we designed culture independent (denaturant gradient gel electrophoresis DGGE) and culture dependent (16S rDNA) methods. The samples for this study were taken from the depths of 1850 m off Barren Island of the Andaman Sea, and 2000 and 1400 m off Chennai and Cudallore of the Bay of Bengal. The phylogenetic analysis, based on 16S rDNA sequence data, has suggests their affiliation to three major phyla viz. Firmicutes (48%), Proteobacteria (30%, alpha and gamma-class) and Actinobacteria (22%). Bacillus was the most frequently isolated genus. This is the first report on the isolation of Brucella, Fictibacillus, Mesorhizobium and Cobetia spp. from deep sea sediments. Eleven of the 34 operational taxonomic units probably represents new species. To investigate the metabolic potential, the isolates were screened for production of the extracellular hydrolytic enzyme and antibacterial compound. Almost 91% of isolates showed production of at least one of the extracellular hydrolytic enzymes, such as caesinase, alpha-amylase, urease, gelatinase, lipase and DNase. Streptomyces was the only genus which showed antibacterial activity. This study highlights that the examined deep sea environment could be a hot spot for microbial derived natural products. [ABSTRACT FROM AUTHOR]