Xenopus tropicalis is an important model animal in immunology. Based on the available genome data, the genomic organization of all three light chain gene (ρ, σ and typeⅢ) loci were recently characterized in Xenopus tropicalis. On the basis of similarity of protein sequences, genomic organization and chromosomal location of the light chain genes among frogs and mammals, the data strongly support the previous suggestions that the ρ genes belong to the κ gene lineage, whereas the typeⅢ genes share a common origin with the λ genes. About 200 cDNA fragments from each of ρ, σ and typeⅢ genes, were cloned and sequenced respectively generating 22, 25 and 44 clones that have unique VJ junctions (after removal of redundant clones). Recombined VJ junctions of cloned light chain cDNA were analyzed, which showed a paucity of N and P nucleotides in expressed ρ, σ and typeⅢ genes. They also show that somatic VJ rearrangements of the σ gene seemed to be dependent on short stretches of homologous nucleotides (microhomology). The microhomology-directed VJ recombination obviously results in very limited diversity. However, most expressed ρ and typeⅢ VJ junctions showed direct ligation or deletions of V and J coding ends. These results help researchers to understand the generation of Ig diversity in X. tropicalis.