We estimate that Neocalanus tonsus makes a contribution to downwards carbon flux of 1.7–9.3 g C m–2 year–1, in subantarctic waters, the Subtropical Front and waters immediately to the north, based on its ontogenetic vertical migration minus the biomass of eggs, the products of which are returned to the surface the following season. This flux is an order of magnitude greater than that estimated (0.27 g C m–2 year–1) for vertical migration of large copepods in the North Atlantic. Over the total 55.6 × 106 km2 where N. tonsus is distributed, 0.17 Gt C year–1 are estimated to be lost annually to the ocean interior. In subantarctic water, this loss represents 1.4% of primary production and is 14% greater than the measured sedimented particulate organic carbon (POC) at 300 m. Similarly, in subtropical water, carbon loss to the ocean interior from N. tonsus seasonal migration is estimated to be 13% lower than measured POC flux. Nevertheless, N. tonsus was never found in time-incremental sediment trap samples. We hypothesize that the apparently proportionally different role of downwards seasonal migration of large copepods relative to sedimented POC in the North Atlantic compared with the subarctic North Pacific and Southern Ocean arises because of a combination of differences in the nutrient status of these oceans, differences in the rate of development of grazer populations in spring, and differences in life history characteristics of large copepods. The flux due to the behaviour of N. tonsus in different parts of its range, put into the context of the estimated global-mean net flux of 1.7–3.7 g C m–2 year–1 taken up by the ocean, may be a regionally significant amount. The summer downward migration of N. tonsus, however, does not entirely explain the observed seasonal variation in regional measurements of pCO2 off New Zealand.