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The dark ocean is one of the largest biomes on Earth, with critical roles in organic matter remineralization and global carbon sequestration. Despite its recognized importance, little is known about some key microbial players, such as the community of heterotrophic protists (HP), which are likely the main consumers of prokaryotic biomass. To investigate this microbial component at a global scale, we determined their global abundance and biomass in meso- and bathypelagic waters in samples from the Malaspina-2010 circumnavigation using a combination of epifluorescence microscopy and flow cytometry. HP were clearly ubiquitous in the global deep ocean, even at the deepest 4000 m samples investigated. Their abundances decreased with depth, from an average of 72 ± 19 cells mL-1 in mesopelagic waters to 11 ± 1 cells mL-1 in bathypelagic waters, whereas their global biomass decreased from 280 ± 46 to 50 ± 14 pg C mL-1. The parameters that better explained the variance of HP abundance were depth and prokaryote abundance, and to lesser extent oxygen and the abundance of large viruses. Different signs suggested active grazing of HP on prokaryotes, such as the presence of flagella in most cells, and the generally good correlation with prokaryote abundance. On a finer scale, the prokaryote:HP ratio in abundance varied at a regional scale, and sites with the highest ratios appear related to a larger contribution of osmotrophy to flagellate nutrition. Our study is a step forward towards determining the relationship between HP and their environment, unveiling their importance as players in the dark ocean's microbial food web.