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Lotus is a taxonomically problematic genus that includes several agriculturally important species as well as the model legume L. japonicus. We have studied relationships among 39 Lotus species representing 11 of 14 sections of the genus using sequences of two nuclear ribosomal DNA regions (ITS and ETS) and two plastid DNA regions (psbA-trnH spacer and rps16 intron). Both nuclear and plastid markers highly support segregation of sections Lotea, Krokeria, Pedrosia s.l. and Chamaelotus. On trees constructed using nuclear markers, section Chamaelotus occupies an unresolved basal position in the genus, while on plastid trees it is close to members of sections Pedrosia and Heinekenia. The number of large clades on trees obtained by different markers varies, however there is a clade whose taxonomic composition is very stable in all phylogenetic trees. It includes members of sections Lotea, Tetragonolobus, Krokeria, Pedrosia and non-monophyletic Heinekenia. Within this clade the section Tetragonolobus is close to section Lotea on nuclear trees and to section Heinekenia on plastid trees. The most controversial are phylogenetic relationships among sections Lotus, Dorycnium, and Bonjeanea. Nuclear markers suggest a monophyly of both section Lotus and a group that includes members of the former genus Dorycnium (sections Dorycnium and Bonjeanea). According to plastid data, section Lotus is subdivided into two or three separate groups which are mixed with members of sections Dorycnium and Bonjeanea in one large clade. On plastid trees, Dorycnium and Bonjeanea form several groups not corresponding to their previous taxonomic circumscription.