Coccolithophores and Parmales are important functional groups of calcified and siliceous marine nanophytoplankton. Large-scale biogeographic distributions of the two groups were investigated based on 71 samples that were collected in the Atlantic Ocean. Using a scanning electron microscope, a total of 48 taxa of coccolithophores and eight taxa of Parmales were recorded, with Emiliania huxleyi, Tetraparma pelagica and Triparma strigata as the predominant forms. The highest abundances of coccolithophores (376 × 103 cells l−1) and Parmales (624 × 103 cells l−1) were observed in waters north-east of the Falkland Islands and the South Georgia Island, in close association with the Subantarctic Front and Polar Front, respectively. Three major biogeographic assemblages, i.e. the Falkland Shelf Assemblage, the Southern Ocean Assemblage and the Atlantic Ocean Assemblage, were revealed in cluster analysis. Additionally, canonical correspondence analysis indicated that temperature significantly affects the latitudinal patterns of the two algal groups. High abundances of Parmales were closely coupled with those of E. huxleyi in waters of the Southern Ocean with low temperature (<10°C). However, the number of coccolithophore species, along with the Shannon–Weaver diversity, significantly increased with elevated temperature, suggesting more diverse assemblages in tropical waters.