The present invention relates to an underwater harvesting system (1) for harvesting zooplankton or mesoplagic fishes, comprising an underwater vehicle (2) for being lowered into the sea and towed behind a surface vessel (3), comprising a housing (21) provided with an inlet (22) through which zooplankton-containing-fluid may flow; a hose (4) mounted on the underwater vehicle and in fluid communication with the inlet, the hose being adapted to secure and fluidly connect the underwater vehicle to the surface vessel; and pumping means for drawing in a zooplankton-containing-fluid through the inlet in the underwater vehicle and for pumping the zooplankton-containing-fluid through the hose to the surface vessel. The invention further relates to a method for harvesting zooplankton or other marine organisms.