Hordeum murinum L. is a polyploid complex of thermophilic, annual, zoochoric grasses of Mediterranean–Irano- Turanian origin that is commonly present in Europe. H. murinum complex includes three annual and most often autogamous taxa: glaucum, leporinum and murinum. The variation of nuclear microsatellites, chloroplast microsatellites and chloroplast SNP-based PCR-RFLP markers of H. murinum from Europe was analyzed in order to investigate its migration. The chloroplast markers revealed three distinct haplotypes. Two of them are characteristic of leporinum and murinum. A geographical pattern of haplotypes has been detected, however it does not correspond to the known patterns of migration routes in the Holocene. Geographic distribution of genotypes defined by nuclear microsatellites has shown a geographic trend that may link the migration of leporinum and murinum with the spread of Neolithic agriculture in Europe. This study also confirms genetic distinction of glaucum, as well as genetic uniformity of murinum and leporinum.