Sclerotinia stem rot is the main disease of rapeseed. Up to date, genes involved in defending Sclerotinia sclerotiorum have not been found in rapeseed and some other related plants. In order to reveal the disease resistance mechanism, we inoculated Sclerotinia sclerotiorum on the stems of resistant variety Ning RS-1 and susceptible one APL01, and compared eleven defensive related genes' expression profiles between two varieties during the period of inoculation by using fluorescence quantitative PCR. Results showed that four genes(PGIP, Cu/ZnSOD, OXO, and GLP) were highly expressed both in Ning RS-1 and APL01, and the expression in Ning RS-1 was much higher than that in APL01. Especially, PGIP's expression at 24 hours after inoculation(hai) with Sclerotinia sclerotiorum was 170.4 times as high as that at 0 hai in Ning RS-1, while it was only 3.5 times in APL01, and PGIP's expression in Ning RS-1 was 1299.4 times as high as that at 24 hai in APL01. Two genes(LOX2 and PDF1.2) were expressed low both in Ning RS-1 and APL01, but with significant difference between two varieties. Five genes(FeSOD, PAL, EDS1, PR1, and EIN3) were also expressed low in Ning RS-1 and APL01, and without significant difference between two varieties. We inferred that the reason of resistance against Sclerotinia sclerotiorum in Ning RS-1 is related to the up-regulated expression of PGIP, which prevents the PG protein in pathogen from degrading the cell wall of infected host tissues, resulting in the inhibition of incidence and spread of sclerotinia stem rot in rapeseed.