The diploid Lotus japonicus was previously suggested as a model for the legume plant family. We present here the nucleotide sequence and the derived gene organization of a small part of the genome in this model plant. Two functional genes with the same transcriptional orientation were identified within the 23326-bp genomic region analysed. The LjGln1 gene encodes a cytosolic glutamine synthetase and the LjKrm (Kinesin repeat motif) gene encodes a polypeptide with similarity to a repeated motif present in the microtubule-associated kinesin light chain protein. Transcripts of the glutamine synthetase gene are found primarily in roots and root nodules, while transcripts of the Krm gene are found in roots, root nodules and leaves. In the region between Gln1 and Krm, the presence of a third gene, Pge1, was suggested by analysis with the Grail exon recognition program. Upstream of the Gln1 gene a segment carrying two apparently non-functional, fragmented copia-like retroelements, dRtp1 and dRtp2, was identified. Sequence similarity to reverse transcriptase- and RNaseH-coding regions defined the defective retro-elements dRtp1 and dRtp2 within this segment. Terminal repeats were not found but three different sets of short direct repeats are located adjacent to the dRtp1 element. The three genes and the incomplete retroelements occupy most of the analysed DNA, leaving approximately one-fifth of the chromosome fragment without recognisable genome constituents.