Oxygen Minimum Zones (OMZs) are regions of the ocean with dissolved oxygen concentrations of <20 µM that have formed due to natural processes but are expanding in consequence of climate change. Despite the extreme conditions of low oxygen, OMZs contain unique microbial communities that play key roles in global biogeochemical cycling. In addition, recent research has shown that OMZs also harbor viral communities, which have been discovered with auxiliary metabolic genes (AMGs) that augment host metabolisms and indirectly contribute to these global cycles. Although both microorganisms and viruses have been found in OMZs, it remains unclear how both groups shape and are shaped by physical and environmental gradients in the OMZ water column. In this dissertation, I have used shotgun metagenomic sequencing and bioinformatic tools to investigate both microbial and viral communities in the ocean’s largest and intense OMZ, which resides in the Eastern Tropical North Pacific. In chapter 1, shotgun sequencing was used to identify microbial functional and taxonomic composition in key distinct layers of the water column across different geographical stations in the ETNP OMZ. Read-based analysis showed that gene abundances were much higher in the OMZ core and microbial communities that resided in the productive regions of the OMZ were mainly composed of heterotrophic prokaryotes. Chapter 2 focused on viral communities and AMG composition in the OMZ, along with comparative analysis on metagenomic tools for AMG detection. Main findings from this chapter are that most viruses identified as cyanophage and Pelagibacter phage, while most AMGs were involved in photosynthesis and purine synthesis. Lastly, Chapter 3 focused on induvial Metagenome Assembled Genomes (MAGs) of ammonia oxidizing archaea (AOA) for comparative genomic analysis. AOA were identified with many different metabolic capabilities and phylogenomic analysis showed AOA formed distinct clades, each sharing and containing unique core functional genes. Overall, the results within this dissertation demonstrate that both microbial and viral community composition and functionality correlate with key biogeochemical gradients in the ETNP OMZ, and contribute to the field of microbial and viral ecology through metagenomic analysis.