Septoria speckled leaf blotch (SSLB), caused by Septoria passerinii Sacc., and net form net blotch (NB), caused by Pyrenophora teres f. teres Drechsler, are fungal diseases that decrease the yields of barley in the Upper Midwest. An effective way to manage these diseases is to plant resistant cultivars. To characterize the genetics of resistance to both pathogens, two advanced barley breeding lines, one resistant to NB (M120) and another resistant to SSLB (Sep2-72), were crossed, creating a population of 115 recombinant inbred lines. The two parents and the population were evaluated in three greenhouse seedling assays for each pathogen and for simple-sequence repeat and diversity arrays technology markers. Composite interval mapping revealed two major quantitative trait loci (QTL) associated with NB on chromosome 6H, located in bins 2 and 6. The QTL located in bin 6 explained 19 to 48% of the phenotypic variation and the QTL located in bin 2 explained 25 to 44% of the phenotypic variation. A new locus for resistance to SSLB, Rsp4, was identified on chromosome 6H, located in bins 3 to 4. Mapping these genes in elite breeding germplasm will accelerate the development and utilization of marker-assisted selection to enhance resistance to these diseases.