Abstract. The distribution of lipid biomarkers and their stable carbon isotope composition was investigated on suspended particles from different contrasting trophic environments at six sites in the South East Pacific. High algal biomass with diatom-related lipids (24-methylcholesta-5,24(28)-dien-3β-ol, C₂₅ HBI alkenes, C_16:4 FA, C_20:5 FA) was characteristic in the upwelling zone, whereas haptophyte lipids (long-chain (C₃₇-C₃₉) unsaturated ketones) were proportionally most abundant in the nutrient-poor settings of the centre of the South Pacific Gyre and on its easter edge. The dinoflagellate–sterol, 4α-23,24-trimethylcholest-22(E)-en-3β-ol, was a minor contributor in all of the studied area and the cyanobacteria-hydrocarbon, C₁₇n-alkane, was at maximum in the high nutrient low chlorophyll regime of the subequatorial waters near the Marquesas archipelago.

The taxonomic and spatial variability of the relationships between carbon photosynthetic fractionation and environmental conditions for four specific algal taxa (diatoms, haptophytes, dinoflagellates and cyanobacteria) was also investigated. The carbon isotope fractionation factor (ε_p) of the 24-methylcholesta-5,24(28)-dien-3β-ol diatom marker, varied over a range of 16% along the different trophic systems. In contrast, ε_p of dinoflagellate, cyanobacteria and alkenone markers varied only by 7–10‰. The low fractionation factors and small variations between the different phytoplankton markers measured in the upwelling area likely reveals uniformly high specific growth rates within the four phytoplankton taxa, and/or that transport of inorganic carbon into phytoplankton cells may not only occur by diffusion but also by other carbon concentrating mechanisms (CCM). In contrast, in the oligotrophic zone, i.e. gyre and eastgyre, relatively high ε_p values, especially for the diatom marker, indicate diffusive CO₂ uptake by the eukaryotic phytoplankton. At these nutrient-poor sites, the lower ε_p values for haptophytes, dinoflagellates and cyanobacteria indicate higher growth rates or major differences on the carbon uptake mechanisms compared to diatoms.