In this thesis double digest restriction-site associated DNA sequencing was established for the marine microalgae Alexandrium tamarense and microsatellite marker analysis as well as 28S analysis of four A. tamarense populations was performed. A. tamarense belongs to the phylum dinoflagellata, a large group of flagellate protists with unique features in respect to their genome structure and cell organization. Furthermore this microalga is responsible for a lot of HABs. A group of three morphologically very similar species form the A. tamarense” species complex”, which is further subdivided into five distinct ribotype groups. Questions like the biogeography of this species complex as well as the question how to bring molecular data about separation of clades and morphological characteristics of defined species in line remain partly unsolved by now. Special emphasis in this thesis lays on the biogeography of ribotype group I of the A. tamarense species complex. Previous studies addressing the above mentioned questions used molecular markers which cover just a tiny fraction of the genome. ddRADSeq produces a lot more markers leading to a higher coverage of the genome and thus a much higher resolution for molecular ecological studies. In order to provide results for comparison with ddRADSeq, analysis were performed with an already established marker system. Hence microsatellite analysis with 10 microsatellite loci was performed. The four tested populations were from 3 different geographic origins: Alaska, Greenland and Northsea. Principle Coordinate and Structure analysis were performed to reveal inter- and intrapopulation structuring. A Mantel´s test was conducted to test if geographic distance correlates with genetic distance. The ddRADSeq approach could be established successfully. Results from microsatellite analysis revealed separation of Alaska´s population into two distinct clusters in Structure as well as in PCoA analysis. These findings support previously proposed models of biogeographic distribution of the group I ribotye from the A. tamarense species complex.