The trophic community structure of the zooplankton is important in determining the routes by which the primary production (PP) is channelled through the pelagic trophic web, with implications on the carbon exported. The main objective of this doctoral thesis is to determine the role of appendicularians in coastal marine food webs. Emphasis is given to the processes of differential removal of autotrophic biomass, production and fate of faecal matter, and discarded appendicularian houses. The present research involved the comparison of two different marine ecosystems where appendicularians are an important component of the zooplankton community: 1) a boreal system, represented by the Gullmar Fjord in the West-Coast of Sweden (58° 18 N - 11° 32 E) y 2), and the coastal upwelling area of Mejillones Bay, in the northern Humboldt Current System off Chile (23° S - 70° W). The ingestion rate of appendicularians on different size-spectra of primary producers, protozoan and bacteria was estimated. Results were compared with the impact of crustacean zooplankton. Faecal pellet and appendicularian house production in the water column were determined. Vertical carbon fluxes derived from faecal matter and deserted houses were quantified, and these results were compared with the fluxes mediated by other zooplankton. The methodology used involved a combination of field measurements, with metabolic rates estimated in the field and in the laboratory (e.g. size-fractioned ingestion rates, bacterophagy, faecal pellet and house production rate, etc.). All these measurements were carried out during oceanographic cruises in October 1999 and March 2000 in the Gullmar Fjord (West-coast Sweden), and during October 2000, February, August and October 2001 in Mejillones Bay (northern Chile). The appendicularian Oikopleura sp. was one of the dominant filter-feeding zooplankton groups during phytoplankton blooms occurring in both areas. Results showed that a high abundance of large cells increases appendicularian house production, which may involve an increase in the appendicularian-mediated vertical flux of carbon. In both areas, appendicularians were feeding mainly on bacteria and nanoflagellates. Large cells were removed, but they only remained attached to the houses, therefore most of these large cells were not ingested. Grazing impact of appendicularians was higher in Gullmar Fjord than in Mejillones Bay. Only a small percentage of the high PP observed in this embayment (0.1–0.3 %) was removed by the appendicularians. A high contribution of fecal pellets and appendicularian houses to the vertical carbon fluxes was estimated in Gullmar Fjord. An insignificant percentage of the PP estimated in Mejillones Bay was exported out of the photic layer by the zooplankton activity (< 0.3 %). In this area, the mean transfer of carbon through mesozooplankton-mediated food webs was relatively inefficient, and a significant percentage of the PP (16–18 %) was removed by the protozooplankton (through ‘microbial loop’ pathway). The main contribution of appendicularians to the carbon flux in these coastal areas was the removal of bacteria and small cells from the water column, and its export out of the euphotic layer through faecal pellets and ‘marine snow’ derived from their deserted houses. This mechanism was especially effective in shallow waters, where a high % of the faecal matter and/or aggregates produced by appendicularians might be exported to the benthos, due to their short residence time in the water column, low destruction and degradation by the pelagic community.