To investigate the relationship between genetic distance (GD) and hybrid performance, two types 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 parental varieties of Brassica napus from different geographical origins. Hybrids were produced in a NCⅡ mating design by hand-pollination. The result indicated that 25 parental varieties (lines) could be divided into six groups 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 another group, SI-1310 and varieties from foreign countries could be separated into other three groups. The grouping was generally consistent with parental pedigrees and geographical origins. Significant differences in yield, 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 the determination coefficient was low. It appeared to be unsuitable for using the genetic distance based on SSR and ISSR markers to predict heterosis and hybrid performance in Brassica napus. To investigate the relationship between genetic distance (GD) and hybrid performance, two types 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 parental varieties of Brassica napus from different geographical origins. Hybrids were produced in a NCⅡ mating design by hand-pollination. The result indicated that 25 parental varieties (lines) could be divided into six groups by Un-weighted Pair SI-1300 and SI-1320 could be singly clustered into one group, respectively. Varieties from China could be separated into another group, SI-1310 and varieties from foreign countries could be separated into The threeing groups are generally consistent with parental pedigrees and geographical origins. Significant differences in yield, quality and phenological period trai ts were observed among these parent groups. It was significantly unsuitable for using the genetic distance based on SSR and ISSR markers to predict heterosis and hybrid performance in Brassica napus.