Several larger vertebrate species have recovered from dramatic bottlenecks caused by overhunting and habitat destruction. One of the most notable comebacks concerns the Eurasian beaver (Castor fiber L.), which has increased its range by natural dispersal from both relict populations and populations established through translocations. Genetic methods have recently been used to study beavers at several locations. However, owing to a lack of reference samples from relict populations and alternative names of mitochondrial DNA haplotypes, the ancestry of re-established beaver populations remains obscure. Here, we focus on the genetic characterization of several newly established populations. Unlike previous studies, we also used microsatellite genotypes of reference samples from all relict populations. Our analysis was fully capable of tracing the origin of the nuclear and mitochondrial genome to relict populations. Although we confirmed an extraordinarily low genetic diversity in relict populations, our analysis showed restored diversity in newly established populations resulting from translocations. Recent expansions and stochastic effects have created a strong but complicated population structure, with neighbouring populations differing significantly in genetic composition. We conclude that this restored genetic diversity very likely contributes to the viability and ongoing expansion of the newly established populations.