The Tnt1 retrotransposon of tobacco (Nicotiana tabacum) has proven to be a very efficient mutagen for the model legume Medicago truncatula ecotype 108 and cultivar Jemalong 2HA and for economically important plants, such as soybean and potato. In this study, the activity of Tnt1 in the model legume Lotus japonicus L. was tested. First, a new regeneration and transformation protocol was developed for L. japonicus that represents a new tool for legume mutagenesis and reverse genetics. Using this protocol, the Tnt1 retrotransposon was introduced into L. japonicus by Agrobacterium tumefaciens-mediated transformation, and primary transgenic lines, named starter lines, were constructed. In vitro regeneration via indirect somatic embryogenesis using starter lines harboring two to eight copies of the transgene resulted in new Tnt1 transposition events. The Tnt1 retrotransposon remained inactive during plant growth and in the T-1 progeny, indicating that it is well suited for insertional mutagenesis in L. japonicus.