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 where they play an active role in the degradation of carbohydrates. However, their role in processing other abundant biomolecules in the ocean in comparison with that of prokaryotes remains enigmatic. Here, we performed a global-ocean multi-omics analysis of all fungal-affiliated proteases (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. We found that pelagic fungi are active contributors to protein and carbohydarte degradation and thus of carbon and nitrogen cycling in the global ocean. Dothideomycetes are the main fungi responsible for protease activity in the surface layers, whereas Leo- tiomycetes dominate in the mesopelagic realm. Fungal proteases gene abundance, diversity, and expression increased with increasing depth, similar to fungal CAZymes. 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. In-depth analysis of the most widely expressed fungal protease revealed the potentially dominating role of saprotrophic nutrition in the oceans. Our findings reveal a widespread active role of oceanic fungi in the cycling of carbon (carbohydrates) and nitrogen (proteins), highlighting potentially different ecological niches occupied by fungi and prokaryotes in the global ocean.