Prochlorococcus, the smallest but most abundant marine primary producer, plays an important role in carbon cycling of the global ocean. As a phototroph, Prochlorococcus is thought to be confined to the euphotic zone, with commonly observed maximum depths of ~150-200 m, but here we show for the first time the substantial presence of Prochlorococcus populations in the dark ocean ("deep Prochlorococcus" hereafter). Intensive studies at the Luzon Strait in the western Pacific Ocean show that the deep Prochlorococcus populations are exported from the euphotic zone. Multiple physical processes including internal solitary waves could be responsible for the transportation. These findings reveal a novel mechanism for picoplankton carbon export other than the known mechanisms such as sinking of phytodetritus and aggregates or grazing-mediated transportation. © Author(s) 2014.