Background Reduction of genetic diversity can lead to reduced fitness of species, such as the loss of adaptability to changing environments. The native Eurasian beaver (Castor fiber) was hunted to extinction from Finland and many other countries in Europe in the nineteenth century. In Finland, the species was reintroduced in the 1930s with only a few individuals from Norway. Re-introductions were performed also in other countries of northern Europe and as a result, Eurasian beaver populations have undergone population bottlenecks leading to low levels of genetic diversity. Materials and Methods Here, 200 Eurasian beaver samples from Finland, Estonia, Lithuania, and Russian Karelia were investigated using 12 microsatellite markers to examine the level of genetic diversity and relationship between the populations. Results While Russian and Estonian populations were genetically the closest, the Finnish population was clearly distinct from all others and had the lowest genetic variability among the study populations. This may be deleterious to the population especially in a changing environment. Conclusions Genetic rescue could be the best solution to increase the genetic diversity and improve the future prospects of the population, although more studies are required to resolve the optimal source population.