Fusarium head blight of wheat is a major deterrent to wheat production world-wide. The genetics of FHB resistance in wheat are becoming clear and there is a good understanding of the genome location of FHB resistance QTL from different sources such as Sumai3, Wuhan, Nyubai and Frontana. All the components needed for assembling complex genotypes through large-scale molecular breeding experiments are now available. This experiment used high throughput microsatellite genotyping and half-seed analysis to process four independent crosses through a molecular breeding strategy to introduce multiple pest resistance genes into Canadian wheat. This included two backcrosses and selection for a total of six FHB resistance QTL, orange blossom wheat midge resistance (Sm1) and leaf rust resistance (Lr21). In addition, the fixation of the elite genetic background was monitored with 45-76 markers to accelerate restoration of the genetic background at each backcross. The strategy resulted in 87% fixation of the elite genetic background on average at the BC2F1 generation and successfully introduced all of the chromosome segments containing FHB, Sm1 and Lr21 resistance genes. The molecular breeding strategy was completed in 25 months, at an equal pace to conventional crossing and selection of spring wheat.