Parastagonospora nodorum is a necrotrophic fungal pathogen that causes the disease Stagonospora nodorum blotch (SNB) on wheat. The fungus produces necrotrophic effectors (NEs), that when recognized by corresponding host genes, cause cell death leading to disease. A novel NE, designated SnTox7, was identified from culture filtrates of isolate Sn6 of P. nodorum. SnTox7 is a small protein with estimated size less than 30 kDa. The interaction between SnTox7 and its corresponding host sensitivity gene, Snn7, explained 33% of the disease variation among a segregating F2 population. The Snn7 gene governs sensitivity to SnTox7 and was delineated to a 2.7 cM interval on the long arm of wheat chromosome 2D. Another host sensitivity gene Snn3- B1, conferring sensitivity to SnTox3, was previously mapped on the short arm of wheat chromosome 5B. Forty-four molecular markers were added to the genetic map to saturate the Snn3-B1 gene region. High-resolution mapping of the Snn3-B1 locus in 5,600 gametes delineated the gene to a 1.5 cM interval. The closely linked markers should be very useful for marker-assisted selection against Snn3-B1. A third host gene, Snn1, confers sensitivity to the NE Tox1. Snn1 was isolated through map-based cloning, and its structure, expression and allelic diversity were further characterized. A bacterial artificial chromosome (BAC) contig of about 2.5 Mb in size was identified to span the Snn1 locus through screening of Chinese Spring chromosome arm 1BS minimum tiling path (MTP) pools. Additional markers developed from BAC end sequences (BESs) delineated the Snn1 gene to a physical segment consisting of four BAC clones. Sequencing and bioinformatic analysis of these clones led to the identification of seven candidate genes. Six of the seven candidates were excluded through critical recombinants. The seventh gene, a cell wall-associated kinase (WAK), was verified as Snn1 through comparative sequence analysis with ethylmethane sulfonate (EMS)-induced mutants. The Snn1 transcription profile showed that it was regulated by light and possibly circadian rhythms. These results demonstrate that P. nodorum can hijack multiple host pathways driven by different classes of genes that typically confer resistance to biotrophic pathogens, thus demonstrating the surprisingly intricate nature of plant-necrotrophic pathogen interactions.