To investigate the relationship between genetic distance (GD) and hybrid performance, twotypes of molecular markers, microsatellites (simple sequence repeats, SSRs) and intro-simple sequence repeats(ISSRs), were employed to detect the genetic diversity of 3 double low self-incompatible lines and 22 male pa-rental varieties of Brassica napus from different geographical origins. Hybrids were produced in a NC Ⅱ mat-ing design by hand-pollination. The result indicated that 25 parental varieties (lines) could be divided into sixgroups by Un-weighted Pair Group Mathematics Average (UPGMA) clustering based on GDs. SI-1300 and SI-1320 could be singly clustered into one group, respectively. Varieties from China could be separated into an-other group, SI-1310 and varieties from foreign countries could be separated into other three groups. Thegrouping was generally consistent with parental pedigrees and geographical origins. Significant differences inyield, quality and phenological period traits were observed among these parent groups. Although hybrid yield/plant showed significantly positive correlation with genetic distance based on SSR and ISSR markers, but thedetermination coefficient was iow. It appeared to be unsuitable for using the genetic distance based on SSR andISSR markers to predict heterosis and hybrid performance in Brassica napus.