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Genus Lotus includes ca. 130 species of annual and perennial herbs, semishrubs and small shrubs of the tribe Loteae (Leguminosae). The genus is widely distributed in the Old World and has the main diversity center in the Mediterranean, from where the genus presumably originated. Lotus includes several species complexes, i. e. groups of species with complicated structure and unclear interspecific boundaries. Our study was focused on the genetic structure in two species complexes of the northern evolutionary branch of the genus Lotus. Lotus dorycnium s. l. is a complex of taxa traditionally regarded as members of Dorycnium, however molecular phylogenetic data support placement of the complex in the genus Lotus. The complex has a wide Mediterranean range, extending in the north to Central and Eastern Europe, and in the east to the Crimea, the Caucasus, and the Western Caspian region. The results of the morphological analyses demonstrated some degree of differentiation, with some taxa (treated as subspecies) more or less well defined, whereas the others hardly distinguished from each other. Analyses of the L. dorycnium complex based on nrITS revealed a tendency towards a geographic differentiation into Western, Eastern, and South-Eastern (=Turkish) groups. Phylogenetic and phylogeographic analyses of the same set of specimens using concatenated plastid markers trnL-F, rps16, and psbA-trnH demonstrated a low resolution between the L. dorycnium complex and L. hirsutus, as well as among the taxa within the L. dorycnium complex, which can be interpreted as evidence of an incomplete lineage sorting or hybridization. The haplotype network of the L. dorycnium complex is branched, with many missing/hypothetical haplotypes and a predominance of singletons. The evolutionary processes responsible for incongruence in phylogenetic signals between plastid and nuclear sequences of the morphologically well-defined species L. dorycnium and L. hirsutus were most likely localized in the Eastern Mediterranean. A possibility of rare gene exchange between the L. dorycnium complex and the group of L. graecus is also revealed. Another studied complex of species from the genus Lotus is the L. corniculatus complex. The geographical range of the complex includes the Mediterranean basin, the high mountains of eastern sub-Saharan Africa, all of Europe (except the northernmost Arctic regions) and southwestern, central and eastern Asia. A haplotype network for this complex was constructed using cpDNA trnL-F region. Several important differences can be outlined between cpDNA haplotype networks of L. dorycnium and L. corniculatus species complexes, associated with their different evolutionary histories. It is assumed that the origin of both complexes is associated with the Mediterranean, and then the members of the complexes spread to more northern and eastern regions. Some representatives of the L. corniculatus complex have migrated much further to the north and east (up to Southern Siberia and North-Western China) and have undergone a recent expansion there, as evidenced by the presence of widespread haplotypes and a low number of derived haplotypes. In contrast, most subspecies of L. dorycnium apparently existed for a long time in the Mediterranean region, undergoing fluctuations in abundance, as evidenced by the presence of many missing haplotypes and the multimodal distribution of pairwise substitutions. We hypothesize that L. dorycnium ssp. herbaceus may have undergone a relatively recent expansion to the east as evidenced by the unimodal mismatch distribution.