Biodiversity research has been established as an important field in ecological studies and is used to define evolutionary relationships and species interactions within complex ecosystems. Environmental change impacts the composition and biodiversity of species in the environment tremendously. Consequently, a species removal or addition can change the ecosystem functioning and stability and will influence biogeochemical cycles. Here, the overaiming objective was the biodiversity observation within Greenland and Iceland, and its relationship with ecosystem functioning. Furthermore, the aim was to identify at which degree biodiversity can be used to characterize different areas, and be used as a describer for evolutionary relationships and species interactions within ecosystems. The 454-sequencing technology increased the DNA sequencing throughput, due to massive parallelization through emulsion PCR (emPCR) and sequence analysis on fiber optic chips. The amplicon sequencing approach offered to pool a number of samples (amplicons) using barcodes for identification. The diversity from different size fractions (micro-, nano-, eukaryotic and bacterio- picoplankton) was assessed using the 28S hypervariable D1/D2 region, or the 16S rDNA. Sequencing results were analyzed by the MG-Rast pipeline for species assignment. The diversity was appraised using the inverse Simpson’s index (DS−1), species composition and nonmetric multidimensional scaling (NMDS). Additionally, dissolved organic matter (DOM) analysis of the same water samples was done. The biodiversity distribution within the Greenlandic and Icelandic sampling transect differed with the size fractions, but no driver, other than size separation itself, could be found. With smaller size fraction a higher diversity was observed, as well as higher similarities between Greenland and Iceland. The diversity differences between the regional separated areas, were highly influences by temperature and salinity, but also silicate and phosphate had an influence. Higher temperatures and salinities in Iceland resulted in a high presence of dinoflagellates, and due to higher silicate and phosphate concentrations in Greenland diatoms were more present in this area. Bacterioplankton size fractions revealed little information, due to a focus on the phyla distribution. DOM was analyzed with NMDS, and revealed high similarities between the two areas. The altered multivariate analysis ’metaMDS’ was an efficient and compact method to observe biodiversity differences and indirect included environmental factors. Higher sampling is needed to explain variation directly through of environmental parameters by constrained analysis. Further analyses are needed to confirm the results in this study, and comparing the results will advance the understanding of biodiversity and regional factors determining the species composition. Relating the molecular DOM data with biodiversity patterns could reveal tracers for species composition to observe the changing biogeochemical cycles on a larger scale.