Ecogenomics is an advanced approach to biodiversity research that can serve to define evolutionary relationships and species interactions within complex ecosystems. Current hypotheses propose that impacts of environmental changes on the biodiversity, composition and bioactivity of species are particularly pronounced in Arctic regions. Our study focused on the comparison of molecular biodiversity of four planktonic size-fractions (micro-, nano-, pico- and bacterioplankton) in coastal waters of Greenland and Iceland, and the consequences for ecosystem functioning. Molecular diversity was assessed via sequencing the 28S hypervariable D1/D2 region, or the 16 rDNA for 454 amplicon sequencing. Metatranscriptomic data were assessed using Illumina 100 paired-end technology. We showed that biodiversity distribution within the two areas differed markedly within and among size-fractions. In general, we observed a higher diversity, as well as higher similarities between Greenland and Iceland station transects, within smaller size-fractions. Diversity differences between the regions were highly correlated with temperature and salinity, but also with silicate and phosphate concentrations impact. This pattern was also reflected in activity profiles deduced from the metatranscriptomic analyses.