Over the last two decades, several large-scale ocean sequencing projects have generated significant insights into the functional diversity of ocean microbes. Yet, we still lack a unifying collection of ocean microbiomes from pole to pole and from the surface ocean to the deep sea. Here, we generated 43,191 newly recovered prokaryotic genomes, spanning 138 phyla with a novel phylum identified at hydrothermal vents. We constructed a unified global ocean microbiome catalogue (GOMC) by integrating the newly recovered genomes and public marine microbial genomes from previous studies, which includes 24,195 species-level genomes, extending previous know microbial phylogeny by more than 2-fold. Intriguing microbial community structure patterns were also revealed showing that microbial community composition is more constrained by depth than ocean boundaries. Large scale functional profiling of GOMC revealed many novel Biosynthetic Gene Clusters, antimicrobial peptides, uneven distribution pattern of CRISPR-Cas systems and their complex interactions with antibiotic resistant genes across different phylogeny and various ecosystems. Gene mining of deep-sea microbes, which were characterized by the highest level of biological novelty, uncovered four enzymes which efficiently degrade polyethylene terephthalate as confirmed by in-vitro experiments. Thus, the GOMC is the most comprehensive marine microbial genomics resource to date and therefore not only extends global biodiversity, but also serves for sustainable bioprospecting of microbial life especially from the underexplored deep sea.