Phytoplankton is responsible for approximately 50 % of the annual global primary production and Emiliania huxleyi ((Lohm.) Hayard and Mohler) is an important part of the phytoplankton community. It contributes to the biological- and carbon counter-pump and therefore species success of E. huxleyi might play an important role on vertical carbon fluxes in the ocean. Several studies have shown that E. huxleyi is susceptible for Global change. Emiliania huxleyi has a high adaptive capacity and can thrive in highly diverse but also stable environments from the subtropics to subpolar regions. Emiliania huxleyi has a biphasic life cycle with phenotypically distinct haploid and diploid cell stages interconnected by syngamy, a form of sexual reproduction. A recent study unveiled that E. huxleyi populations subjected to stable environments had a significant proportion of strains which have lost key genes associated to haploid cell formation. The loss of sex implies several evolutionary constraints for species survival and adaptive capacity, since asexual reproducing lineages tend to possess a loss of heterozygosity. However with an increase of homozygosity deleterious alleles can be unmasked and the fitness of a given species can be reduced. As a counterpart acts here ameiotic recombination, which can retain adaptive capacity in asexual lineages, by balancing the emergence of deleterious alleles. As asexual and sexual populations of E. huxleyi from the same geographic origin, we further expect sympatric evolution of the two subpopulations, due to separation of their gene pools. Aim of this study was to unravel the influence of demographic, ecological as well as environmental factors on the population differentiation as well as to uncover mechanisms which influence micro-evolutionary processes in Asexual E. huxleyi lineages. As method of choice we used a reduced representation sequencing approach called double digest Restriction site Associated DNA (ddRAD) sequencing, where only genomic regions between two different restriction enzyme cutting sites were sequenced. For 1 population from Peru and 3 populations from Chile basic population genetic parameters were assessed as well as genomic erosion and Gene Diversity in asexual Chile strains within and between populations. Based on basic population genetic parameters, moderate genetic differentiation between Peru and Chile populations was detected, most likely explained due to separation of the populations by different water masses and currents. However indications for the presence of sympatric evolution of asexual and sexual gene pools were given as well. The observed heterozygosity in Asexual E. huxleyi strains was not reduced although inbreeding indices were elevated, which could indicate a loss of heterozygosity. Therefore it remains unresolved which micro-evolutionary processes are dominating the genomic evolution of asexual E. huxleyi strains. The overall exceptionally high interspecific genetic diversity of E huxleyi might mitigate effects of Asexual reproduction and helps to sustain a high adaptive capacity.