Value of the data •This data provides comprehensive leaves and roots glucosinolate profiles across a diversity panel of 288 Brassica napus (oilseed rape) genotypes with information on the population structure. Glucosinolate trait data can benefit oilseed rape agribusinesses and researchers of this field in the selection of genotypes with desirable profiles or manipulation of profiles to modulate plant-pest interactions. •The GEM and SNP markers identified in the region of the genome that controls the variation in glucosinolate contents can help accelerate breeding of oilseed rape by marker-assisted selection •This data could be used for comparison or replication of genetic association markers for the natural glucosinolate variations in other populations and other plant tissues.