Phytoplankton biomass, through its proxy, Chlorophylla, has been assessed at synoptic temporal and spatial scales with satellite remote sensing (RS) for over two decades. Also, RS algorithms to monitor relative size classes abundance are widely used; however, differentiating functional types from RS, as well as the assessment of phytoplankton structure, in terms of carbon remains a challenge. Hence, the main motivation of this work it to discuss the links between size classes and phytoplankton groups, in order to foster the capability of assessing phytoplankton community structure and phytoplankton size fractionated carbon budgets. To accomplish our goal, we used data (on nutrients, photosynthetic pigments concentration and cell numbers per taxa) collected in surface samples along a transect on the Atlantic Ocean, during the 25th Atlantic Meridional Transect cruise (AMT25) between 50° N and 50° S, from nutrient-rich high latitudes to the oligotrophic gyres. We compared phytoplankton size classes from two methodological approaches: (i) using the concentration of diagnostic photosynthetic pigments, and assessing the abundance of the three size classes, micro-, nano-, and picoplankton, and (ii) identifying and enumerating phytoplankton taxa by microscopy or by flow cytometry, converting into carbon, and dividing the community into five size classes, according to their cell carbon content. The distribution of phytoplankton community in the different oceanographic regions is presented in terms of size classes, taxonomic groups and functional types, and discussed in relation to the environmental oceanographic conditions. The distribution of seven functional types along the transect showed the dominance of picoautotrophs in the Atlantic gyres and high biomass of diatoms and autotrophic dinoflagellates (ADinos) in higher northern and southern latitudes, where larger cells constituted the major component of the biomass. Total carbon ranged from 65 to 4 mg carbon m–3, at latitudes 45° S and 27° N, respectively. The pigment and cell carbon approaches gave good consistency for picoplankton and microplankton size classes, but nanoplankton size class was overestimated by the pigment-based approach. The limitation of enumerating methods to accurately resolve cells between 5 and 10 μm might be cause of this mismatch, and is highlighted as a knowledge gap. Finally, the three-component model of Brewin et al. was fitted to the Chlorophylla(Chla) data and, for the first time, to the carbon data, to extract the biomass of three size classes of phytoplankton. The general pattern of the model fitted to the carbon data was in accordance with the fits to Chladata. The ratio of the parameter representing the asymptotic maximum biomass gave reasonable values for Carbon:Chlaratios, with an overall median of 112, but with higher values for picoplankton (170) than for combined pico-nanoplankton (36). The approach may be useful for inferring size-fractionated carbon from Earth Observation.