The recent discovery of Russian wheat aphid demonstrates the potential impact of pest incursions into Australia, and the absence of resistant cultivars that can be easily deployed. Further, there is no incentive for wheat breeding companies to develop resistant varieties due to the cost burden and low return on investment. Here, we report on research undertaken at ICARDA and CIMMYT, which indicates that the Australian wheat industry is very vulnerable to damage from certain pests, especially Hessian fly (zero resistance), Karnal bunt (3.6% resistance) and Sunn pest (1.5% resistance). Although these pests and pathogen are not currently present in Australia, much of the Australian cereal cropping regions offer an acceptable climate for the pests to establish. The purpose of our research is to reduce the risk of potential future economic loss to wheat growers due to incursion by providing wheat breeders with molecular markers and parental genetic stocks that carry genes for resistance to Karnal bunt, Hessian fly and Sunn pest. Using conventional breeding methods, elite Australian breeding lines have been developed that combine resistance to the exotic pests and fungal disease with good agronomic qualities. In addition, data is being generated to determine whether any deleterious traits have transferred from landraces along with the resistance genes. To further assist uptake of the newly developed resistant germplasm, molecular markers have been developed, and validated. We have identified single-nucleotide polymorphisms in the dirigent-like protein-encoding gene (HfrDrd), and the wheat Hessian fly responsive proteins Hfr-1 and Hfr-2, to aid pre-emptive breeding for Hessian fly resistance. In addition, we have identified a major gene locus (Ei1) for pre-emptive breeding against Sunn pest, and gene-based markers on chromosomes 6B and 3A for Karnal bunt resistance. The resistance data, parental genetic stocks and associated diagnostic markers are freely available to the public through online access.