Phototrophic microbial eukaryotes dominate primary production over large oceanic regions. Due to their small sizes and slow sinking rates, it is assumed they contribute relatively little to the downward export of organic carbon via the biological pump. Therefore, the community structure of phototrophic cells in the deep ocean has long been overlooked and remains largely unknown. In this study, we used an integrative approach, including epifluorescence microscopy, sequencing of 18S rRNA and photosystem-II psbA gene transcripts, to investigate phototrophic microbial eukaryotes in samples collected from the tropical Western Pacific Ocean. It was found that: 1) pigmented nano-sized eukaryotes (PNEs) are ubiquitous in the deep Western Pacific Ocean down to 5,000 m depth; 2) the PNE community is dominated by cells 2-5 µm in size; 3) their abundance is significant, averaging 4 ± 1 (± s.e.) cells mL-1 in waters below 1,000 m which is comparable to that of heterotrophic nanoflagellates; 4) the active pigmented microbial eukaryotes in the deep waters are highly diverse and dominated by Haptophyta followed by Chlorophyta and Bacillariophyta; 5) PNEs in deep waters were likely transported from surface ocean by various fast-sinking mechanisms, thus contributing to the biological pump and fueling the deep-sea communities by supplying fresh organic carbon.