Calcareous nannofossils provide biostratigraphic age-markers for Pleistocene Arctic Ocean sediments. However, Pleistocene Arctic sediments are dominated by fine-grained terrigenous material, and commonly contain rare and poorly preserved coccolith specimens that can be difficult to identify under the light microscope (LM). Using paired observations of the same specimens under LM and a scanning electron microscope (SEM), we recently discovered that poorly preserved Noelaerhabdaceae specimens that cannot be identified at the species level were previously classified as Gephyrocapsa huxleyi using LM observations alone. Moreover, the visual resemblance under LM between G. huxleyi and another Quaternary marker species, Pseudoemiliania lacunosa, also led to occasional misdiagnosis. Given the importance of G. huxleyi and P. lacunosa for stratigraphic age control, this has potentially profound implications for our understanding of the paleoceanographic history of the Arctic, and also other ocean basins. This study focuses on challenges met in improving and applying the paired LM-SEM technique for observation of the same nannofossil specimens, and on its subsequent adjustments in the case of Quaternary Arctic sediments, which often contain low abundances of calcareous micro- and nannofossils. Moreover, we review morphological aspects and discuss potential difficulties in unambiguously identifying G. huxleyi, P. lacunosa and Gephyrocapsa under LM and illustrate the need of integrating SEM images – which can be difficult to obtain in low-diversity assemblage sediments dominated by silt and clay.