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Phylogenetic analyses of the genus Lotus revealed early split into "south" and "north" lineages. Phylogenetic relationships within the "north" lineage, which includes members of the section Lotus and those of the former genus Dorycnium, are the most controversial and will be discussed with special emphasis to the position of problematic species. Species of the Lotus “north” lineage were previously classified in sections Lotus, Dorycnium and Bonjeanea (Degtjareva et al., 2006). We studied phylogenetic relationships within this lineage using nrITS and three plastid DNA regions. The evolution of the group is essentially homoplastic. The reasons for this homoplasy are not clear. Modern or ancient hybridization, incomplete lineage sorting, high level of genetic variability may be considered as possible reasons. The monophyly of the genus Lotus (incl. Dorycnium and Tetragonolobus) was repeatedly confirmed, while segregation of Dorycnium at generic level was not supported (Degtjareva et al., 2006; Kramina et al., 2016). Each of the sections composing the “north” lineage is also non-monophyletic. Lotus section Bonjeanea looks artificial according to both DNA markers. It includes two species (i.e., L. rectus and L. strictus) of unclear relationships, and their origin is probably connected with early divergence of the “north” lineage. The third species of the section Bonjeanea (i.e., L. hirsutus) evidently demonstrates close relationships with Lotus section Dorycnium. The core group of the sections Dorycnium and Lotus (i.e., L. dorycnium complex and L. corniculatus complex, respectively) are well distinguished, however other small species groups of those sections reveal incongruent relationships in different analyses. The monophyly of the L. corniculatus complex is clearly demonstrated by all markers, while L. dorycnium complex is monophyletic by nrITS only. Phylogenetic position of several other Lotus groups (i.e., section Canaria, newly discovered species related to L. conimbricensis, and others) and genetic geographical structure of some groups are discussed.