The detection and characterization of genetic variability at the infraspecific level is of great importance for the understanding of numberous ecological and evolutionary questions, such as speciation, gene flow, etc. The level of genetic diversity determines a species' ability to respond to changes in its environment and therefore its success in nature. Molecular markers are the tools of choice to answer these questions about biodiversity and two types of markers are especially suited to be used in phycology.Microsatellites are short repetitive sequences of 1-6 bp (e.g., [CT]n or [ATG]n) that occur in all living organisms and have shown to be excellent molecular markers for population studies because of their high degree of polymorphism and relative simplicity to use and analyse, even though their development is time-consuming. Microsatellite markers are under development or already available for a number of important phytoplankton species, i.e., the coccolithophorid Emiliania huxleyi. The DNA fingerprinting technique called Amplified Fragment Length Polymorphism (AFLP) is another possibility for studying biodiversity in phytoplankton species. The advantages of this marker type lie in their high number of potentially polymorphic bands and that no prerequisite knowledge about the genome of the investigated species is needed, which makes them fast to establish. AFLP markers have been used, for example, for studies of the dinoflagellate Alexandrium tamarense.With these markers, detailed studies of population genetics, spatial and temporal changes in population structure and the interaction of genotypes with different biotic and abiotic factors are possible.