The phylogeography and evolutionary history of the long-distance migratory Eurasian Reed Warbler Acrocephalus scirpaceus were analysed using sequence data from the mitochondrial DNA COI gene of 405 individuals and cyt b sequences from a subset of those individuals from 20 breeding, migrating and wintering populations over its wide geographical range. Median-joining network and Bayesian phylogenetic analyses recovered three lineages corresponding to three subspecies of A. scirpaceus that started to diverge approximately 480 000 years ago: one spanning Asia (Acrocephalus scirpaceus fuscus), one encompassing Europe and Northern Africa (Acrocephalus scirpaceus scirpaceus) and a third that included Eastern Africa and Southwestern Asia (Acrocephalus scirpaceus avicenniae). Phylogenetic analyses suggest that the third clade is basal and diverged from its sister species, the African Reed Warbler Acrocephalus baeticatus, around 700 000 years ago. This earliest subspecies (avicenniae) may have survived the Last Glacial Maximum in one of the African refugia, probably the low forest refugium of the Ethiopian Highlands. Sequences of 348 samples from Germany, which were captured for ringing, showed that one bird was genetically assigned to the subspecies fuscus, the first genetic evidence of this Asian subspecies in Central Europe. According to our DNA sequences, 6.8% of Eurasian Reed Warblers were misidentified at the species level, Marsh Warbler Acrocephalus palustris accounting for most of these misidentified specimens. At the subspecies level, of 22 fuscus identified by genetic analyses, only six had been correctly named by the ringers.