Xanthomonas oryzae pv. oryzicola (Xoc) and X. oryzae pv. oryzae (Xoo) are the causal agents of bacterial leaf streak and bacterial blight of rice, respectively. Xoc possesses extracellular protease activity (ECPA), but Xoo does not contain ECPA. Previously, a Tn5 transposon-mediated mutation library was generated and 12 ECPA-deficient mutants of Xoc was obtained. These mutant lost extracellular protease activity completely or partially, and show reduced virulence in rice. In the present study, these mutant were characterized and the Tn5 insertion site were determined. One mutant had a disruption in ecpA gene (ecpAXoc) encoding extracellular protease was studied further. EcpAXoc is required for extracellular protease activity and full virulence of Xoc. Expression of ecpAXoc is induced in the presence of rice cells. Purified EcpAXoc has protease activity and induced chlorosis- and necrosis-like symptoms when infiltrated into rice leaves. Both the N-terminal and C-terminal regions of EcpAXoc are important for protease activity. A frame shift in ecpAXoo coding sequence abolishes ECPA in Xoo and make EcpAXoo non-functional. Collectively, these results suggest that EcpAXoc is a tissue-specific virulence factor for Xoc but not Xoo.