The phylogeographical structure amongst 39 populations of the temperate forest plant Carex pilosa in Europe was studied using amplified fragment length polymorphism (AFLP), polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), and sequencing of non-coding regions of plastid DNA. No plastid DNA polymorphisms were found within almost the entire 14 000 bp investigated, and it seems that chloroplast sequence analysis is not appropriate for studying the migration history of this species. The AFLP data also showed no clear genetic pattern. Marginal separation of central and north-eastern European populations did not allow for the detection of glacial refugia in this species. Rare AFLP fragments showed no association with geography and led to speculations regarding the possibility of glacial survival of C. pilosa in microenvironmentally suitable patches in central Europe. This is in accordance with recent palaeopalynological and macrofossil evidence. © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society, 2008, 158, 115–130.