The diatom species Fragilariopsis kerguelensis is endemic to the Southern Ocean where it plays a key role in the ocean silica cycle due to its heavily silicified cell walls. Frustules from dead cells can sink to the ocean floor and therefore contribute about 90% to the diatom frustules making up the Antarctic opal belt, a band of heavily silicified sediments below the Antarctic Circumpolar Current. Recent studies showed that two morphotypes of F. kerguelensis can be found in core samples originating from the Southern Ocean. The morphotypes can be distinguished by the morphometric descriptor rectangularity and the abundance of the morphotypes can be linked to the origin of the samples from glacial or interglacial periods. It is, however, so far unknown whether these morphotypes also occur in current diatom assemblages of the Southern Ocean; if yes, how their occurrence is influenced by environmental conditions; and whether they represent different species, or rather phenotypic plasticity within a single species. For answering these questions diatom valves in water and sediment samples from the Southern Ocean, preserved on microscopic slides were analysed morphologically using a semi automated morphometry workflow. Histograms of the rectangularity were then plotted which all showed a bimodal distribution proving the existence of the two morphotypes in recent samples. In the next step the biogeographic distribution pattern of the two morphotypes was assessed by plotting the rectangularity distribution at each sample station. Whereas one morphotype was dominant in the northernmost samples, its dominance decreased towards the south, and the other morphotype became dominant in the southernmost locations investigated. This pattern could also be linked to the Sea Surface Temperature with a regression. After the previous findings the question arose if the morphotypes could be cryptic species or if they occur due to phenotypic plasticity within a single species. To answer this a genetic assessment with diatom strains showing different rectangularity values, isolated from the Southern Ocean and kept in live cultures at the Alfred-Wegener-Institut was done. Their ribosomal internal transcribed spacer (ITS) regions were amplified using PCR and then analysed with Sanger sequencing. The results made it possible to identify three potential species based on their genetic differences. One semi-cryptic species was solely made up of morphotype B whereas morphotype A was divided in two genetic clusters representing two cryptic species. Mating experiments were carried out to uncover possible reproductive barriers between the cryptic species. The results showed, that strains being assigned the same cryptic species commonly sexually reproduce, whereas sexual reproduction between strains from different cryptic species was only observed in a few exceptions. In summary, the two investigated morphotypes of Fragilariopsis kerguelensis can be found in the Southern Ocean today, with one dominating at higher, the other at lower Sea Surface Temperatures. Comparison of ribosomal ITS sequences and mating experiments indicate that the two morphotypes seem to belong to three different species, one semi-cryptic species belonging to one and two cryptic species to the other morphotype.