Tan spot, caused by Pyrenophora tritici-repentis (Ptr), is an economically important disease on both common wheat (Triticum aestivum L.) and durum (T. turgidum L. ssp. durum). Genetics of resistance to tan spot is complicated and needs to be further investigated for breeding cultivars with more complete resistance. The objective of this study was to map and characterize genetic resistance in two wheat bi-parental popuations. In Louise × Penawawa population, four quantative trait loci (QTL) were identified and the major race-nonspecific QTL, designated as QTs.zhl-3BL, was shown to have epistatis and additive effect on Ptr ToxA-Tsn1, Ptr ToxC-Tsc1 interactions, respectively. Nine QTL were identified in the Lebsock × PI 94749 population with three likely being novel. This work improves our understanding of genetic resistance to tan spot and provides important tools for breeding resistant cultivars.