Abstract. The distribution of ultraphytoplankton was investigated in the western North Pacific Subtropical Gyre (NPSG) during La Niña, a cold phase of El Niño Southern Oscillation (ENSO). Observations were conducted in a north-south transect (33.6–13.25° N) along the 141.5° E meridian in order to study the ultraplankton assemblages in various oligotrophic conditions. Analyses were performed at the single cell level by analytical flow cytometry. Five ultraphytoplankton groups (Prochlorococcus, Synechococcus, picoeukaryotes, nanoeukaryotes and nanocyanobacteria-like) defined by their optical properties were enumerated in three different areas visited during the cruise: the Kuroshio region, the subtropical Pacific gyre and a transition zone between the subtropical Pacific gyre and the Warm pool. Prochlorococcus outnumbered the other photoautotrophs in all the investigated areas. However, in terms of carbon biomass, an increase in the relative contribution of Synechococcus, picoeukaryotes and nanoeukaryotes was observed from the centre of the subtropical gyre to the Kuroshio area. In the Kuroshio region, a peak of abundance of nanoeukaryotes observed at the surface suggested an increase in nutrients likely due to the vicinity of a cold cyclonic eddy. In contrast, in the salinity front along the isohaline 35 and anticyclonic eddy located around 22.83° N, the mainly constant distribution of Prochlorococcus from the surface down to 150 m characterised the dominance by these microorganisms in high salinity and temperature zone. Results suggested that the distribution of nanocyanobacteria-like is also closely linked to the salinity front rather than low phosphate concentration. The maximum abundance of ultraphytoplankton was located above the SubTropical Counter Current (STCC) at depths > 100 m where higher nutrient concentrations were measured. Finally, comparison of the ultraphytoplankton concentrations during El Niño (from the literature) and La Niña (this study) conditions seems to demonstrate that La Niña conditions lead to higher concentrations of Synechococcus in the Subtropical gyre and a lower abundance of Synechococcus in the Kuroshio region. Our results suggest that the west part of NPSG is a complex area, where different water masses, salinity fronts and eddies lead to a heterogeneous distribution of ultraphytoplankton assemblages in the upper layer of the water column.