Diatoms are successful in occupying a wide range of ecological niches and biomes along the global ocean. Although there is a recognized importance of diatoms for the Southern Ocean ecosystems and biogeochemical cycles, the current knowledge on their ecology and distribution along the impacted Antarctic coastal regions remains generalized at best. HPLC-CHEMTAX approaches have been extensively used to this purpose, providing valuable information about the whole phytoplankton community, even for those small-size species which are normally difficult to identify by light microscopy. Despite that, the chemotaxonomic method has reserved minimal focus on great diversity of types associated with diatom genera or species. Here, we show a coupling between the key genera and the corresponding chemotaxonomic subgroup type-A or type-B of diatoms via HPLC-CHEMTAX and microscopic analysis, using chlorophyll-c 1 and chlorophyll-c 3 as biomarker pigments, respectively. The results demonstrated strong correlations for nine of the fifteen most abundant diatom genera observed along the Northern Antarctic Peninsula, from which five (four) were statistically associated with chlorophyll-c 1 (chlorophyll-c 3). Our study highlights the importance to observe diatoms in greater detail, beyond being only one functional group, for a better understanding on their responses under a climate change scenario.