The Arctic treeline ecotone is a large environmental gradient covering a vast area in Siberia. It sensitively reacts to changes in the environment, which is observable, for instance, in he responding vegetation. The vegetation across the treeline is known to influence the water chemistry of thermokarst lakes in this region. Sensitive algae, such as diatoms, respond to these changes and thus, diatom compositions correlate with the surrounding vegetation. Most studies on the diatom compositions across the treeline ecotone used the classic morphological approach, whereas little is known about the genetic diversity and composition of diatoms. In this Master study NGS sequencing data were used to analyze the diatom composition of 32 lakes and two lake sediment cores in comparison to morphological data sets. Furthermore, the correlation of diatom assemblages with environmental factors was analyzed and compared to morphological data. All analyses were conducted on two taxonomic levels, i.e. species and genera, in order to check the taxonomic resolution of the analyses. The results showed a significant relationship between the diatom composition and specific environmental parameters, i.e. DOC and maximal depth for both methodologies. Calcium and sulfate also had a significant influence on the genetic obtained data, while hydrogen carbonate and conductivity had a significant influence on the morphological data. It was possible to gain similar results with both approaches regarding the diatom compositions of both the recent and the ancient sediment material. Furthermore, it could be shown that there are only slight differences between the taxonomic assignment on species and genus level in the genetic approach, due to incomplete reference databases. Altogether, it could be concluded that even though the analyzed and compared methods are very different, their results are highly comparable.