A backcross population derived from a cross between the dominant genic male sterile line Rs1046A and the double-low cultivar 'Samourai' was used for linkage map construction in Brassica napus. A linkage map with a total length of 2 646 cM was developed using 138 AFLP markers, 83 SSR markers and one morphology trait, which were distributed over 18 major linkage groups, two triplets and one linkage pair. 11.7% of the mapped markers distorted from the expected 1:1 ratio. The dominant genic male sterility gene (Ms) was mapped in LG10 and surrounded by five closely linked AFLP markers. Meanwhile,two evident marker segregation distortion regions were observed in both LG8 and LG16. The map constructed in the present study and the mapping of Ms gene are highly valuable in designing marker-assisted breeding program for the genic male sterile two-type line in Brassica napus. They are also important to map-based cloning of the Ms gene and to better understanding of the mechanism of genic male sterility at molecular level.