Peripheral populations of the wels catfish Silurus glanis in Sweden have suffered from severe declines during the last centuries. Presently, the species persists in only a few isolated water systems in southern Sweden. Here, we used whole genome sequencing to assess the genetic status of the three remaining native populations (lake Baven, river Eman and lake Mockeln) as well as one reintroduced population of admixed origin (Helgea).