Anthropogenic perturbations and climate change are severely threatening habitats of the global ocean, especially in the Arctic region, which is affected faster than any other ecosystem. Despite its importance and prevailing threats, knowledge on changes in its micro- and nanoplanktonic diversity is still highly limited. Here, we look back almost two decades (May 1–26, 2002) in order to expand the limited but necessary baseline for comparative field observations. Using light microscopy, a total of 196 species (taxa) were observed in 46 stations across 9 transects in the Greenland Sea. Although the number of observed species per sample ranged from 12 to 68, the diversity as effective species numbers (based on Shannon index) varied from 1.0 to 8.8, leaving about 88% as rare species, which is an important factor for the resilience of an ecosystem. Interestingly, the station with the overall highest species number had among the lowest effective species numbers. During the field survey, both number of rare species and species diversity increased with decreasing latitude. In the southern part of the examined region, we observed indications of an under-ice bloom with a chlorophyll a value of 9.9 μg l⁻¹ together with a nitrate concentration < 0.1 μM. Further, we recorded non-native species including the Pacific diatom Neodenticula seminae and the fish-kill associated diatom Leptocylindrus minimus. Our comprehensive dataset of micro- and nanoplanktonic diversity can be used for comparisons with more recent observations and continuous monitoring of this vulnerable environment—to learn from the past when looking towards the future.