<i>Prochlorococcus</i>, the smallest but most abundant marine primary producer, plays an important role in carbon cycling of the global ocean. As a phototroph, <i>Prochlorococcus</i> 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 <i>Prochlorococcus</i> populations in the dark ocean ("deep <i>Prochlorococcus</i>" hereafter). Intensive studies at the Luzon Strait in the western Pacific Ocean show that the deep <i>Prochlorococcus</i> 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.