The membrane-bound fatty acid desaturases (FADs) play vital roles in regulating plant fatty acid (FA) compositions which directly affect oil quality in rapeseed (Brassica napus L.). In the present study, a total of 68 putative FAD genes were identified in the crop and were phylogenetically clustered into four subfamilies. Genomic localization revealed that the genes were distributed across 21 chromosomes at various densities. The structures of paralogous genes were considerably conserved in the number of exons and in the length of introns. It was found that the expansion of the B. napus FAD family was mainly attributable to whole genome duplication and segmental duplication. Rapeseed seedlings were grown hydroponically under three levels (0, 250, and 500 μM) of cadmium (Cd) and three levels (0, 50, and 100 mM) of salinity. After one week of treatment, the roots and leaves of seedlings were harvested to study the expression patterns of 68 selected BnFADs in response to the different stresses. The results from qRT-PCR analyses suggested that the FAD genes in rapeseed were differentially expressed under various abiotic stresses. The transcript levels of the FAD genes ADS4.8, ADS4.9, ADS4.10, ADS9.1 and SLD8 in the leaves of Cd-tolerant cultivar ZD619 were significantly higher than those in the leaves of sensitive cultivar ZD622 under the 250 μM Cd stress condition. Moreover, the expression levels of 8FAD genes (ADS4.1, ADS4.4, ADS4.9, ADS9.1, ADS9.2, SLD8, FAD7.4 and FAD7.5) in ZD619 roots were obviously enhanced with the increase of salinity concentrations. These results indicate the likelihood of FAD genes involved in Cd and salinity tolerance. This study provides insight on membrane-bound FAD genes involvement in tolerance to abiotic stresses and would provide some more candidate genes for the crop improvement.