We estimate the energy flow through meso-and bathypelagic chaetognaths in the Atlantic sector of the Southern Ocean from (1) depth-structured chaetognath abundance and body mass data, (2) a general chaetognath respiration model driven by body mass, temperature, water depth and taxon, and (3) published relationships between respiration, production and consumption in chaetognaths. In the 500 to 2000 m depth layer chaetognaths have a mean biomass of 0.109 mg Cm-3 in summer and 0.146 mg C m-3 in winter. Chaetognaths respiration and consumption amount to 282 and 563 mg C m-2 yr -1, respectively. Thus, Antarctic midwater chaetognaths consume 0.05% of the copepod standing stock per day or 1% of the daily copepod production in summer. About 2.8% (= 1.9 g C m-2 yr-1) of the net annual primary production is required to fuel the midwater chaetognath community via herbivorous copepods. When assuming a 1: 1 diet of herbivorous and carnivorous copepods, this share increases to 6.1% (= 4.1 g C m-2 yr -1) of annual primary production. It is estimated that chaetognath consumption for the whole water column is 1.4 g C m-2 yr -1. This corresponds to 7.1 % (= 4.8 g C m-2 yr -1) and 15.5% (= 10.4 g C m-2 yr-1) of the primary production channeled through herbivorous copepods and through herbivorous and carnivorous copepods, respectively. Hence, chaetognaths represent an important link between lower and higher trophic levels. To further unravel their role in the ecosystem, additional studies on the meso-and bathypelagic zooplankton community are needed. © Inter-Research 2010.