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Appendicularians are abundant planktonic filter feeders that play a significant role in the pelagic food web due to their high clearance rates. Their diet and feeding rates have typically been measured as bulk chlorophyll or cell removal, with some attention given to prey size but no differentiation between the microbial phylotypes. Using a combination of in situ and laboratory incubations with flow cytometry and next-generation sequencing, we found species-specific differences in clearance rates and diet compositions of 4 common species: Oikopleura albicans , O. fusiformis , O. longicauda , and O. dioica . While O. albicans most efficiently removed nano-eukaryotic algae, the other smaller species preferentially removed micron-sized pico-eukaryotic algae. Pico- and nano-eukaryotic cells constituted the major food source of the studied appendicularians despite their occurrence in oligotrophic water dominated by prokaryotic cells. Across species, pico- and nano-planktonic microalgae biomass comprised 45 to 75% of the appendicularian diets. Although non-photosynthetic bacteria were removed at lower rates than all other prey groups, their total contribution to the appendicularian diet was not trivial, representing 5 to 19% of the planktonic carbon in the appendicularian diet; pico-cyanobacteria contributed an additional 9 to 18%. Removal rates and efficiencies of pico-eukaryotes were higher than those of prokaryotes of similar size. Strikingly different clearance rates were observed for different prokaryotic phylotypes, indicating that factors other than size are involved in determining the capturability of the cells. Collectively, our findings provide additional evidence for differential retention of microbial prey among mucous-mesh grazers and its substantial effect on the upper-ocean microbial community.