1. Genetic variability among individuals, populations and species represents the basic level of biodiversity and is a prerequisite of adaptive evolution. 2. Adaptive evolution is driven by natural selection that acts at the level of individual phenotypes. 3. Genetic variation can also be used as a tool to study the history of species and populations and to explore their current structure and reproductive strategies. 4. Genetic markers that are presumably neutral to selection are used in measuring connectivity among Baltic populations and their uniqueness compared to those in the neighbouring marine or freshwater habitats. Genetic markers have often revealed the presence of previously unknown cryptic species that are much older than the Baltic Sea. 5. In most taxa studied, some genetic differentiation has arisen post-glacially between the Baltic Sea and North Sea populations, e.g. In the Atlantic herring Clupea harengus and the Atlantic cod Gadus morhua. 6. Despite such differentiation, few of the Baltic organisms are considered as locally evolved endemic taxa. An exception is the partly asexually reproducing brown algal species Fucus radicans, which has evolved locally and now coexists with its ancestor Fucus vesiculosus in the northern Baltic Sea. 7. The unique blue mussel and Baltic clam populations in the Baltic Sea are closely related to Pacific lineages (Mytilus trossulus and Macoma balthica balthica) but are distinct from the neighbouring North Sea populations (Mytilus edulis and Macoma balthica rubra). They have been modified by interbreeding in the transition zone between the Baltic Sea and the North Sea and now constitute hybrid swarms. 8. A current methodological shift from single-gene approaches to genome-wide studies will help in distinguishing genes and patterns of variation that are affected by selection from those that merely reflect population structure and in identifying characters that account for the adaptations to the unique Baltic Sea environment.