Systemic acquired resistance is a form of inducible resistance that is triggered in systemic healthy tissues of local-infected plants. Several candidate signaling molecules emerged in the past two years, including the methylated derivatives of well-known defense hormones salicylic acid (SA) and jasmonic acid (JA). In our present study, the symptom on Cucumber mosaic virus (CMV) infected Arabidopsis leaves in 0.1 mM SA or 0.06 mM JA pre-treated plants was lighter (less reactive oxygen species accumulation and less oxidative damages) than that of the control group. JA followed by SA (JA→SA) had the highest inhibitory efficiency to CMV replication, higher than JA and SA simultaneous co-pretreatment (JA+SA), and higher than a JA or a SA single pretreatment. The crosstalk between the two hormones was further investigated at the transcriptional levels of pathogenesis-related genes. The time-course measurement showed JA might play a more important role in the interaction between JA and SA.