Abstract European grayling, Thymallus thymallus (L.), populations have steadily declined since the mid-1980s, mostly because of habitat degradation and increased predation pressure. To provide guidelines for conservation strategies and future management programmes, delineation of conservation and management units is warranted. Over the last decade, several studies have investigated the phylogeography and population genetic structure of T. thymallus using mitochondrial and nuclear microsatellite DNA markers. However, no study has covered the distribution range of T. thymallus across Europe; thus, a comprehensive survey of the evolutionary history of the species is lacking. This paper synthesises the major findings of the molecular studies and provides guidelines for the conservation and management of genetic resources of T. thymallus. At least five major mtDNA lineages have evolved in geographical isolation during the Pleistocene and these lineages should be recognised as the basic evolutionary significant units for T. thymallus in northern, central and southern Europe. There is also evidence for a high level of admixture among major lineages and sublineages, especially in the contact zones of drainages (e.g. in mainland Sweden and Norway and in central Germany), most probably resulting from a complex process of post-glacial and inter-glacial colonisation and re-colonisation events from different refugia during the Pleistocene ice ages. Based on the microsatellite data, T. thymallus shows a substantial level of inter-population genetic differentiation and, compared with other freshwater fish species, a relatively low level of within-population genetic diversity. The species develops discrete population structure, both within hydrologically connected rivers or lakes on comparatively small scales as well as in large river systems.