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The distribution and transport of chlorophyll a (Chla), particulate (POC) and dissolved (DOC) organic carbon, and the respiratory ETS activity of the microplankton community were studied along a filament-eddy system located in the transition zone between the NW Africa upwelling and Canary Islands waters. Two independent filaments (F1 and F2) stemming from the coastal jet, between Cape Juby and Cape Bojador, merged about 100 km offshore, turning southward and onshore forced by the circulation of a recurrent oceanic cyclonic eddy. In general, the coastal upwelling waters presented higher Chla, but lower POC, DOC and ETS activity than filament waters. However, differences in organic carbon distribution and respiratory activity were observed among stations from the two filaments. The biochemical fields were strongly influenced by a complex sub-mesoscale hydrography resulting from the interaction of cyclonic and anticyclonic island eddies with the filaments. The combined F1+F2 filament system transported 97.1 kg s-1 of excess (non-refractory) total organic carbon (e-TOC), a value comparable to other published estimates from upwelling filaments in the NE Atlantic. About 90% of e-TOC was exported as DOC, since eddy re-circulation precluded the offshore transport of POC. Assuming that the calculated transport of e-TOC is representative of the annual average, the yearly offshore transport (3.1 x 10 9 kg C) would represent about 25% of the upwelling primary production of the region of study.