ABSTRACT.    The distribution of selected organisms was studied along a South-East Pacific transect sampled during the BIOSOPE cruise in 2004. The transect can be divided into three regions of very contrasted trophic status: a high Nutrient Low Chlorophyll (HNLC) zone (mesotrophic) near the equator, the South-East Pacific gyre (hyper-oligotrophic), and the Chile upwelling (eutrophic). Picocyanobacteria containing phycoerythrin as well as autotrophic and heterotrophic eukaryotes in different size ranges (smaller than 2 μm, between 2 μm and 5 μm, and larger than 5 μm) were counted by epifluorescence microscopy after DAPI staining. We also determined the abundance of ciliates and dinoflagellates. All populations reached a maximum in the Chile upwelling and a minimum near the centre of the gyre. Picocyanobacteria peaked at 70 10³ cell ml^-1. In the HNLC zone, up to 50 % of picocyanobacteria were part of colonies. Autotrophic eukaryote and dinoflagellate abundance reached 25 10³ cell ml^-1 and 200 cell ml^-1, respectively. We observed a shift in the size distribution of autotrophic eukaryotes from 2-5 μm in eutrophic and mesotrophic regions to less than 2 μm in the gyre and in the east of the gyre. Ciliate abundance showed a different pattern of distribution. Their maximum concentration was 18 cell ml^-1 in the Chile upwelling. However, their abundance was very low near the HNLC zone and the Marquesas Islands. Heterotrophic eukaryotes accounted for up to 75 % of eukaryotes in the gyre.