Wheat belongs to the three most important cereal crops of the world and is grown under a wide variety of climatic and agricultural conditions. Fungal pathogens represent the most relevant biotic stresses for wheat. These include different rust species, powdery mildew, leaf spots, as well as a number of other diseases that result in reduced grain yield and quality. Recently developed genomic tools allow new approaches to improve breeding for resistance to these pathogens based on a more efficient use of genetic resources. In this chapter, we will focus on the powdery mildew powdery mildew and Stagonospora nodorum blotch diseases and discuss the successful identification of wheat genes determining the outcome of pathogen-host interaction and the development of perfect markers for them. Genomic approaches, including gene cloning, allele mining, transcriptomics and comparative genomics have greatly changed and improved our understanding of molecular wheat-powdery mildew interactions. For the necrotrophic pathogen necrotrophic pathogen Stagonospora nodorum much of the interaction was found to be based on pathogen toxins and host susceptibility genes. The work on specific gene-for-gene interactions gene-for-gene interactions opened new possibilities for more efficient resistance breeding. In addition, the molecular identification of quantitatively acting resistance loci in wheat has made important progress, although only few such genes have been cloned, only one of them each against mildew and Stagonospora nodorum blotch Stagonospora nodorum blotch. However, even at this early stage it can be foreseen that the new knowledge might revolutionize breeding for durable resistance in the near future. The progress made towards a whole genome sequence of wheat together with ongoing developments of high throughput techniques provides a completely new perspective on resistance breeding against these two diseases. © 2014 Springer Science+Business Media Dordrecht. All rights are reserved.