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Lotus japonicus (Regel) Larsen is a model legume for evolutionary developmental studies, which genome was recently sequenced for the major part (Sato et al., 2008). It is a diploid member of Lotus corniculatus complex of the section Lotus. For better understanding evolution of morphological characters and their genetic regulation, it is important to know the taxonomic and phylogenetic relationships of L. japonicus. Geographically, L. japonicus is the most eastern race of the L. corniculatus complex. Morphologically, it is one of the closest taxa to the typical L. corniculatus, so that it is sometimes considered as a variety of the latter. However, L. japonicus possesses a number of specific characters which differentiate it from L. corniculatus s.str. It has 1-2(3) flowers per umbel, long calyx teeth with short narrow parts, trichomes developed especially on leaflet petiolules and calyx teeth. Recently, a new species close to L. japonicus was described from Miyako island (Japan), named L. miyakojimae (Barykina & Kramina, 2006). It differs from the typical L. japonicus by predominantly annual life form and some other characters. Discriminant analysis based on morphological characters showed that two Japanese species were distinct from L. corniculatus and related taxa. Phylogenetic analyses based on nrDNA ITS1-2 sequences revealed three clades formed by members of the section Lotus. Two of them are sister to each other, and the third one is not sister to them and combines members of Lotus, Dorycnium and Bonjeanea sections. L. japonicus and L. miyakojimae are grouping together and form the more distant branch of the ‘Lotus corniculatus clade’. Both species differ from L. corniculatus s.str. by 30 substitutions, including a 8-nucleotide deletion and a 12-nucleotide insertion. From each other L. japonicus and L. miyakojimae differ by one substitution only. The closest species to them are L. burttii and L. krylovii.