One primary goal of breeding programs is the identification and utilization of new resistance genes. Sources of new resistance genes frequently include the wild and the earliest domesticated relatives. In this context, emmer (T. turgidum ssp. dicoccum) represents a useful source of resistance genes for several wheat pathogens. The T. dicoccum accession MG5323 was identified as conferring good level of resistance towards leaf rust, stem rust and powdery mildew. A QTL mapping approach allowed the identification of 6 new resistance loci against stem rust, powdery mildew and leaf rust, where MG5323 acted as donor of resistance alleles. Two regions associated to stem rust resistance were identified. The major QTL was located on chromosome 6B (QSr.gpg-6B) with a phenotypic variance (PV) ranging from 51 to 86.8%. The second QTL, on 4A (QSr.gpg-4A), explained 51.6% of PV. A single dominant gene for powdery mildew resistance was located on 2B (QPm.gpg-2BS) explaining 78.7% of total PV. Analysis of leaf rust response yielded a major resistance gene on 1B (QLr.gpg-1BS), explaining till 50% of the total PV and two additional minor resistance genes located on 7B (QLr.gpg7BL-1 and QLr.gpg-7BL-2), whose explained PV was till 25.33%. Notably, only lines bearing resistant alleles at both QLr.gpg1BS and QLr.gpg-7BL showed effective leaf rust resistance, suggesting a complementary action of the two loci. The release of the T. durum genome sequence as well as its functional annotation and a related anchored global metaQTL analysis were used to determine the physical region of the identified QTLs and to conduct comparative analyses. The stem rust resistance regions ranged from 7.29 Mbp (QSr.gpg-6B) to 10.17 Mbp (QSr.gpg-4A). The genetic confidence interval of QPm.gpg-2B corresponded to 5.72 Mbp encompassing 10 open reading frames related to disease resistance genes. Regarding the regions associated to leaf rust resistance, the QLr.gpg-1BS covered a 12.7 Mbp region in which 4 disease resistance related sequences were identified, whilst the physical regions underlined by QLr.gpg-7BL-1 and QLr.gpg-7BL-2 ranged from 11.06 Mbp to 32 Mbp, respectively. No one of these loci detected in MG5323 co-located with resistance loci already mapped in tetraploid wheat, indicating that we were able to identify novel resistance sources. A fine mapping approach of the two major genes identified for leaf rust and powdery mildew resistance has currently been deployed with the aim of restricting the number of the identified candidates and possibly allowing the isolation of the underlying resistance genes.