The aims of this study were to elucidate the recent evolutionary history and current genetic diversity of wild Peruvian vicuña populations with the intention of identifying demographically independent 'management units' within these populations and to assess the likely genetic effects of past and future management strategies. Twelve populations were sampled throughout the range of habitat and reserve coverage in Peru since they were thought to have had relatively long histories of demographic isolation and were not thought to have been influenced by recent translocations of animals from the Pampa Galeras reserve. Blood or skin samples were collected and analysed with eleven previously published South American camelid (SAC) microsatellite DNA markers (Lang et al., 1996; Penedo et al., 1998). These markers proved highly polymorphic and informative in Peruvian vicuña, with mean expected heterozygosity values over all loci varying between 0.377 (Tarmatambo) and 0.586 (Lucanas 2). A total of 20 private alleles were found which may be explained by the relatively low levels of within population compared with among population diversity and indicates some level of local isolation and genetic drift. Therefore, vicuña populations in Peru seem to possess several interesting genetic features, which are a result of biology, habitat occupancy, evolutionary history and management by people in the recent past. The implications of these results for the future management of the Peruvian vicuña are that there should be four demographic management units North-western Junín, Southern Junín, Central Andes and Puno. Translocations of animals should only be carried out within the same, but not between different management units. Free movement of individuals within localities must be ensured to minimise further inbreeding and genetic drift. © Wageningen Academic Publishers The Netherlands, 2006.