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Phosphite (PHI) has been used in the management of <i>Phytophthora</i> diseases since the 1970s.We assessed the effect of PHI on controlling the incidence of <i>Xanthomonas oryzae pv.oryzae</i> and <i>Pyricularia grisea</i>. As a result, PHI application significantly inhibited the incidence of the diseases. To clarify the molecular mechanism underlying this, a transcriptome study was employed. In total, 2064 differentially expressed genes (DEGs) were identified between control and PHI treatment. The key DEGs could be classified into phenylpropanoid biosynthesis (ko00940), starch and sucrose metabolism (ko00500), and plant hormone signal transduction (ko04075). The expressions of defense-related genes had a higher expression lever upon PHI treatment. This study provides new insights into the mechanism of protection effect of PHI against pathogens.