Abstract Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of bacterial blight disease in rice, is one of the most serious plant pathogens worldwide. In the current analysis, we constructed a protein–protein interaction network of Xoo strain PXO99A with two computational approaches (interolog method and domain combination method), and verified by K-Nearest Neighbors classification method. The predicted PPI network of Xoo PXO99A contains 36,886 interactions among 1988 proteins. KNN verification and GO annotation confirm the reliability of the network. Detailed analysis of flagellar synthesis and chemotaxis system shows that σ factors (especially σ28, σ54) in Xoo PXO99A are very important for flagellar synthesis and motility, and transcription factors RpoA, RpoB and RpoC are hubs to connect most σ factors. Furthermore, Xoo PXO99A may have both cAMP and c-di-GMP signal transduction system, and the latter is especially important for this plant pathogen. This study therefore provides valuable clues to explore the pathogenicity and metabolic regulation of Xoo PXO99A.