Aim: The Holocene history of annual plant species is at best shadowy because, for most, the palaeobotanical data is scarce or absent. Hence, there is limited information on their glacial refugia and postglacial colonisation pathways. Also, little is known how human activity has affected their expansion. Here, we outline the joint influences of postglacial colonisation and recent expansions on the genetic diversity of the continental, sub-halophyte species Atriplex tatarica during the late Pleistocene and the Holocene. Location: Europe. Taxon: Atriplex tatarica (Amaranthaceae) Methods: We analysed 780 individuals from 80 populations throughout the current European distribution range, employing chloroplast DNA sequences and microsatellite markers. Results: Five haplotype lineages were recognised based on the results of the cpDNA phylogenetic analyses. These lineages originated 0.43−0.22 my BP. Bayesian clustering analyses divided populations of A. tatarica into two clusters: (i) populations in the Pannonian Basin and the Bohemian Massif and (ii) populations in the North European Plain, the Balkan Peninsula, the Carpathian Arc and the Pontic region. The ABC approach provided the strongest statistical support for a model proposing refugia in the Balkan Peninsula and the Pannonian Basin. Expansions from these refugia occurred around 7,000 yr BP. Main conclusion: Atriplex tatarica represents a continental species growing exclusively in man-made habitats. It serves as a phylogeographic model for annual ruderal taxa currently spreading in central Europe along highways and representing a large group of alien plant species, the so-called archaeophytes. Atriplex tatarica survived the last glaciation in both a southerly located Balkan refugium and in a more northerly refugium in the Pannonian Basin. From these, the species has colonised Europe as a result of expansion of humans and the anthropogenic climate change. The massive colonisation of central north Europe is very recent, with the expansion estimated to have occurred only hundreds of years ago.