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Lotus is the largest genus of the tribe Loteae. It includes important crop plants and a model legume, Lotus japonicus. Taxonomy of Lotus is complicated, and a comprehensive taxonomic revision of the genus is needed. We have conducted phylogenetic analyses of Lotus based on nrITS data and morphological characters. We have included a lot of species not used in previous molecular (Allan et al. 2003, 2004) and morphological (Arambarri 2000) phylogenetic studies. Most important conclusions are: (1) previous findings that Dorycnium and Tetragonolobus cannot be separated from Lotus at the generic level are well supported; (2) L. creticus should be placed into section Pedrosia rather than into section Lotea; (3) wide treatment of section Ononidium is unnatural; (4) section Lotus, in its traditional circumscription, is not monophyletic; (5) L. aegaeus is closest to L. gebelia; (6) segregation of L. shimperi and allies into section Chamaelotus (Kramina & Sokoloff 2003) is well supported.