The B3 DNA binding domain is commonly found in plant-specific transcription factor, including those involved in auxin-regulated and abscisic acid-regulated transcription. The B3 domain family consists of four subfamilies: auxin response factor (ARF), abscisic acid-insensitive3 (ABI3), related to ABI3/VP1 (RAV) and reproductive meristem (REM). In order to better understand the origin and the diversification of B3 domains in plants, we have searched for the B3 domain in Arabidopsis thaliana genome databases (TAIR), Oryza sativa genome databases (TIGR), EST set for the bryophyte Physcomitrella patens (www.sputnik.btk.fi), green algae Chlamydomonas reinhardtii (www.genome.jgi-psf.org/chlamy) and red algae Cyanidioschyzon merolae (www.merolae.biol.s.u-tokyo.ac.jp). The total number of B3 domains were: 86 in Arabidopsis, 63 in rice, at least eight in the bryophyte and a single hit was found in the green algae. The high number of Arabidopsis B3 genes contrasts sharply with the small number in green algae and bryophyte. The results show that an ancient B3 domain gene underwent a large-scale genomic duplication in Arabidopsis and rice. The aminoacid alignment was first conducted using ClustalW using all default options. Phylogenetic trees were constructed by the Neighbor-joining method using MEGA2.1 and 500 bootstrap replicates were performed. Phylogenetic analysis revealed that the B3 domain family is divided in eight subfamilies: ARF, RAV, ABI3, REM-A, REM-B, REM-C, REM-like1 and REM-like2. The subfamily REM has 15 genes with multiple B3 domains and 8 genes near each other in the chromosome 4. It appear to be the recent tandem duplication. In C. reinhardtii, we found a single gene with the B3 domain in ABI3 subfamily. This indicate that this subfamily includes the first type of B3 domain. In this scenario, after this origin, since three subfamilies (ARF, ABI3 and REM-like 1) were found in bryophytes, this divergence took place early in the evolution of land plants. Both rice (monocot) and Arabidopsis (eudicot) share four subfamilies of B3 domain that can appear before angiosperms. Nevertheless, the other subfamilies are not present in both species. Differenties domains such as AP2 DNA binding domain also appear in green algae, however B3 and AP2 domain are together in the same gene only in Arabidopsis and rice. In sequence, we will investigate how the complexity of genes with the B3 domain evolved in Arabidopsis, through the study of duplication events.