The ocean harbors a huge microbial cell abundance with high diversity. Such oceanic microbes are believed to play a significant role in the cycling of materials such as carbon and nitrogen, and it is of emerging importance to understand their ecology. In addition, because the oceanic environment greatly differs from terrestrial environments such as soil but has not been extensively explored, oceanic microbes should be an attractive source for the discovery of microbial and genetic resources that can be used for industrial applications. However, unfortunately, almost all microbes are currently unable to be cultured in the laboratory. This severely restricts our ability to investigate oceanic microbes using classical culture-based techniques, and our understanding of the microbes in the ocean, especially in the deep-sea zone, has been severely limited. Thanks to the recent development of DNA sequencing technologies and bioinformatics, many culture-independent studies have focused on microbial ecosystems in the ocean, including deep-sea zones. 16S rRNA amplicon sequencing requires comparatively low costs and effort and is now a common approach for studying taxonomic diversity in any environment. To further investigate genetic and genomic features in the community, the most frequently used approach is metagenomics, which relies on whole-genome shotgun sequencing. Probe capture enrichment sequencing is a promising technique that allows us to experimentally condense target genes or genomic regions from bulk metagenomic DNA for efficient sequencing analysis. Beyond nucleotide sequences, epigenomic signatures (DNA chemical modifications such as methylation) have recently become available for analysis by ‘metaepigenomics’, an integrated analysis of metagenomics and epigenomics using third-generation sequencing technologies (e.g., PacBio) without cultivation. In this presentation, I will introduce our recent sequencing-based studies of microbial communities in seawater and sediment corrected from various oceanic areas and zones. Our data-driven studies using modern sequencing technologies and bioinformatics illuminate unique taxonomic, genomic, genetic, and epigenomic diversities, providing novel insights into deep-sea microbial ecology, one of the last frontiers on our planet.