Xanthomonas oryzae pv. oryzae, the causal agent of bacterial blight in rice, interacts with rice plants in a gene-for-gene manner. The specificity of the interaction is dictated by avirulence (avr) genes in the pathogen and resistance (R) genes in the host. To date, no avr genes that correspond to recessive R genes have been isolated. We isolated an avrBs3/pthA family gene, avrxa5, from our previously isolated clone p58, which was originally from strain JXOIII. The avrxa5 gene converted the PXO99(A) strain from compatible to incompatible in rice cultivars containing the recessive xa5 gene, but not in those containing the dominant Xa5 gene. Sequencing indicated that avrxa5, which is highly similar to members of the avrBs3/pthA family, encodes a protein of 1238 amino acid residues with a conserved carboxy-terminal region containing three nuclear localization signals and a transcription activation domain. It has 19.5 34-amino-acid direct repeats, but the 13th amino acid is missing in the fifth and ninth repetitive units. Domain swapping of the repetitive regions between avrxa5 and avrXa7 changed the avirulence specificity of the genes in xa5 and Xa7 rice lines, respectively. This indicates that avrxa5 is distinct from previously characterized avrBs3/pthA members. The specificity of avrxa5 toward recessive xa5 in rice could help us better understand the molecular mechanisms of plant-pathogen specific interactions.