Tan spot (TS) and Septoria nodorum blotch (SNB), caused by Pyrenophora tritici-repentis and Parastagonospora nodorum, respectively, are important fungal leaf-spotting diseases of wheat that cause significant losses in grain yield. In this study, two recombinant inbred line populations, ‘Bartai’ × ‘Ciano T79’ (referred to as B × C) and ‘Cascabel’ × ‘Ciano T79’ (C × C) were tested for TS and SNB response in order to determine the genetic basis of seedling resistance. Genotyping was performed with the DArTseq genotyping-by-sequencing (GBS) platform. A chromosome region on 5AL conferred resistance to TS and SNB in both populations, but the effects were larger in B × C (R2 = 11.2%–16.8%) than in C × C (R2 = 2.5%–9.7%). Additionally, the chromosome region on 5BL (presumably Tsn1) was significant for both TS and SNB in B × C but not in C × C. Quantitative trait loci (QTL) with minor effects were identified on chromosomes 1B, 2A, 2B, 3A, 3B, 4D, 5A, 5B, 5D, 6B, and 6D. The two CIMMYT breeding lines ‘Bartai’ and ‘Cascabel’ contributed resistance alleles at both 5AL and 5BL QTL mentioned above. The QTL on 5AL showed linkage with the Vrn-A1 locus, whereas the vrn-A1 allele conferring lateness was associated with resistance to TS and SNB.