The ascomycete Pyrenophora tritici-repentis (Ptr) causes tan spot of wheat, a devastating foliar disease on both common wheat (Triticum aestivum L., 2n=6x=42, AABBDD) and durum (T. turgidum ssp. durum L., 2n=4x=28, AABB). Ptr is known to produce three necrotrophic effectors (NEs), namely Ptr ToxA, Ptr ToxB and Ptr ToxC, to cause disease by interacting with corresponding host sensitivity genes. However, many studies in the last twenty years have suggested that Ptr produces additional virulence factors. My Ph.D. research focused on further identification and genetic mapping of new virulence genes in Ptr. In Chapter 2, a bi-parental fungal population was developed from a cross between two genetically modified heterothallic fungal strains followed by genotyping, phenotyping and QTL mapping. Two QTLs were identified with one being major and the other being minor, which confer virulence of 86-124 toward a Ptr ToxA-insensitive wheat line. In addition, the multiple copy gene ToxB was mapped to two genetically independent loci with one having five copies and the other having a single copy. In Chapter 3, I further characterized virulence of some Ptr isolates obtained from Chapter 2 that do not produce any known NEs. These isolates should be classified as race 4 but were found to still cause disease on many common wheat and durum cultivars. Using a common wheat host population, I identified several QTLs associated with the reaction to these isolates, which are different from three known host sensitivity gene loci. In Chapter 4, several natural race 4 isolates collected in North Dakota were shown to cause no or little disease on common wheat genotypes but cause disease on durum and other tetraploid wheat. Using a segregating population, I identified several new QTL associated with disease caused by these race 4 isolates, suggesting the presence of new virulence factors in these isolates. My Ph.D. research greatly advanced the understanding of the genetics of host-pathogen interaction in wheat tan spot and provided important information to wheat breeding programs aiming to improve tan spot resistance.