Fungi are important degraders of organic matter responsible for reintegration of nutrients into global food chains in freshwater and soil environments. Recent evidence suggests that they are ubiquitously present in the oceanic water column. However, their role in processing organic matter in the ocean in comparison with that of prokaryotes is lagging behind. Here, we performed a global-ocean multi-omics analysis of all fungal-affiliated peptidases (main enzymes responsible for cleaving proteins) and CAZymes (main enzymes involved in the utilization of carbohydrates). Together, proteins and carbohydrate, constitute the major fraction of marine living and detrital biomass. We determined the abundance, expression, diversity, taxonomic affiliation, and functional classification of the genes encoding all pelagic fungal peptidases from the epi- and mesopelagic layers. Dothideomycetes are the main fungi responsible for protease and CAZyme activity in the surface layers, whereas Leotiomycetes dominate in the mesopelagic realm. Fungal CAZyme and proteases gene abundance, diversity, and expression increased with increasing depth. This contrasts with the total occurrence of prokaryotic peptidases and CAZymes which are more uniformly distributed in the oceanic water column, suggesting potentially different ecological niches of fungi and prokaryotes. Our findings reveal a widespread active role of oceanic fungi in the cycling of C and N, highlighting potentially different ecological niches occupied by fungi and prokaryotes in the global ocean.