The following study describes marine eukaryotic microorganisms of the North-Atlantic around the western coast of Greenland, the north Atlantic waters around the Norwegian Lofotes and in a fjord system of the Swedish west coast. DNA sequences and mRNA gathered from expeditions to the coasts of Greenland, Norway and Sweden were used as data set for a comparative meta-genomic study in order to characterize the compositions of the local marine eukaryotic microorganisms. Furthermore an investigation the impact of abiotic factors like temperature, salinity, depth of the water column and availability of key nutrients on the composition of the population was conducted. Parallel to the assessment of the biodiversity through amplicon sequencing of the 28S ribosomal DNA (rDNA) the biological activities for the three sampling locations was achieved by analysis of the expressed mRNA. As an often reoccurring problem of transcriptomic studies is that the currently available databases do not work reliably for the annotation of sequences from marine environments, a purpose build databank with reference data purely from marine microorganisms was used for the annotation of the sequences in order to achieve a higher yield of annotated sequences. By linking the metagenomic observations and the results from the transcriptomic analysis more in depth insights were achieved that would not possible by either approach on its own, such as interactions between species or the differences between the most abundant species and the most biological active species.