Small phytoplankton, consisting of pico and nano size fractions, are diverse in size and taxonomy. Yet, the differences in their productivity and taxonomic diversity are poorly described. Here, we measured the cell-specific carbon fixation rates of small phytoplankton (picocyanobacteriaSynechococcus, picoeukaryotes and nanoeukaryotes) populations and unveiled their associated community composition in oligotrophic subtropical (ST) and high-nutrient low-chlorophyll (HNLC) subantarctic (SA) waters. We coupled 24 hin situradiolabelled14C incubations to flow cytometry sorting (FCM-sorting) and DNA metabarcoding from the same incubated samples, offering a direct account of the community associated with the carbon fixation rates measured. In both water masses, nanoeukaryotes had the highest cell-specific carbon fixation rate, followed by picoeukaryotes andSynechococcus(2.24 ś 29.99, 2.18 ś 2.08 and 0.78 ś 0.55 fgC cell-1h-1, respectively). The cell-specific carbon fixation rates and growth rates ofSynechococcuswere 3-fold higher in ST compared to SA waters, while the rates of picoeukaryotes and nanoeukaryotes had no significant difference between the biogeochemically contrasting water masses. Despite distinct community composition between picoeukaryote and nanoeukaryote populations, the FCM-sorted picoeukaryote community in SA waters and the nanoeukaryotic community in both ST and SA waters were dominated by taxa with reported phago-mixotrophic strategies (Chrysophyceae, Dinophyceae and Prymnesiophyceae), suggesting phago-mixotrophy might alleviate nutrient stress in iron limited conditions for discrete small photosynthetic eukaryote populations.