In the 19th century, the red deer (Cervus elaphus) population in Sweden experienced a rapid decline in numbers and distribution. A small population was, however, remnant in the southernmost province (Skåne) of the country, presumably corresponding to the nominate form of red deer (Cervus elaphus elaphus Linnaeus, 1758). After management, reintroductions, and supplementary release during the 20th century the Swedish C. elaphus population recovered. The recovery was partially uncontrolled, and included introductions of C. elaphus of continental origin. In northern central Sweden (Jämtland) the current C. elaphus population may stem from natural colonization from Norway and/or from specimens of Swedish origin that have escaped from enclosures. To evaluate the status of the current, partially separated populations, we investigated variation at microsatellite markers in 157 C. elaphus specimens from ten locations in Sweden and Norway. Analyses suggest that the highest-likelihood phylogenetic structure among the individuals sampled is described four distinct genetic clusters: (1) animals from the province of Västergötland in south-western Sweden; (2) deer from the southernmost province of Skåne; (3) deer from the provinces Jämtland, Blekinge, and Västmanland; and (4) Norwegian deer. Cervus elaphus from a captive herd at the Skåne Zoo cluster with deer from Skåne or deer from Västergötland, depending on the method of analysis. A number of populations in Sweden may genetically match the nominate form of red deer (C. e. elaphus). The recently established C. elaphus population in Jämtland seems to stem mainly from escapees from enclosures, with a mixed ancestry from the wild remnant population in Skåne and continental deer, whereas the influx from Norway is minor, if any. Our results show the need for a detailed assessment of genetic differentiation, and emphasize the value of local management plans when planning and managing introductions. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109, 43–53.