The majority of WRKY transcription factors (TFs) play a role in the regulation of defense response in plants. Three WRKY genes, PtrWRKY1, PtrWRKY2 and PtrWRKY3, were previously identified in Poncirus and their expressions were characterized in response to cold and drought in Poncirus and Citrus. In this study, expressions of these WRKY genes were studied in response to infection with two major pathogens of Citrus, Citrus tristeza virus (CTV) and Phytophthora citrophthora, in resistant Poncirus and susceptible pummelo (Citrus grandis) plants. Northern blot analysis showed that the expression of the PtrWRKY1 gene was induced earlier and stronger in Poncirus than in pummelo in response to CTV infection. On the other hand, the expression of the PtrWRKY1 gene was not altered in response to P. citrophthora infection neither in Poncirus nor in pummelo. When the expression of the PtrWRKY2 gene was analyzed, it was repressed by CTV inoculation in Poncirus plants, whereas the expression was not changed in response to CTV infection in pummelo or in response to P. citrophthora inoculation in Poncirus or pummelo. Similarly, the expression of the PtrWRKY3 gene was repressed in Poncirus, but not changed in pummelo by CTV inoculation; however, the expression of the PtrWRKY3 gene was induced in Poncirus, but it was repressed in pummelo in response to P. citrophthora inoculation. The expression analysis of three different WRKY genes revealed that they are differentially expressed in response to CTV and P. citrophthora infection in resistant Poncirus and susceptible pummelo suggesting that they may play a role in disease resistance in Poncirus.