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Lotus comprises ca. 130 species of herbs, semishrubs and shrubs native to the Old World, including important pasture crops and a model legume, L. japonicus. Earlier nrITS‐based phylogenies were incongruent with all taxonomic classifications of the genus. In particular, members of the former genus Dorycnium were unexpectedly placed near species of L. sect. Lotus. The primary goal of the present study is to explore whether the unexpected placement of members of sect. Lotus and the former genus Dorycnium in earlier phylogenetic studies resulted from (1) insufficient taxon sampling and/or (2) the use of only one DNA marker. The rooting of the Lotus phylogeny, its major clades and basic biogeographic patterns are also discussed. This is the first global phylogenetic study of Lotus that uses both plastid and nuclear markers. The nrITS region was analyzed in 155 ingroup specimens representing 98 species of Lotus. Sequences of nrITS, nrETS, psbA‐trnH spacer and rps16 intron were analyzed for 70 ingroup specimens representing 54 species. The placement of the segregate genera Dorycnium and Tetragonolobus in the synonymy of Lotus was confirmed. Analyses of plastid data strongly supported a basal split of Lotus into two clades, one comprising species of sect. Lotus plus those traditionally placed in Dorycnium and the other including the rest of the species. The former clade has a centre of species diversity in Europe and N Asia, and the latter in Macaronesia, Africa and S Asia. Only the "Southern" clade is resolved in analyses of nrITS and nrETS data. Trees inferred from plastid, nrITS and nrETS data shared the occurrence of several smaller clades corresponding to traditionally recognized infrageneric taxa or species groups as well as the occurrence of some well‐supported clades that differ from traditional taxonomic concepts. Several instances of incongruence were documented between nuclear and plastid markers and between the two nuclear markers, possibly resulting from reticulate evolution. The extant geographic patterns of Lotus are likely biased by at least one round of area fragmentation followed by expansion coupled with extensive speciation associated with the complex history of the Mediterranean biome.

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