The two recombinant inbred lines (RIL) populations developed by crossing Almaly × Avocet S (206 RILs) and Almaly × Anza (162 RILs) were used to detect the novel genomic regions associated with adult plant resistance (APR) and seedling or all-stage resistance (ASR) to yellow rust (YR) and leaf rust (LR). Both the populations were evaluated for YR APR in two environments (2018 and 2019) and LR APR in three environments (2018, 2019, and 2020) in the Anza population and two environments (2018 and 2019) in the Avocet population; both the populations were phenotyped for one environment during 2020 for LR and YR ASR and genotyped using high throughput DArTseq technology. A set of 51 QTLs including 22 for YR APR, nine for LR APR, nine for YR ASR, and 11 for LR ASR were identified. Also, a set of 13 stable QTLs including nine QTLs (QYR-APR-2A.1, QYR-APR-2A.2, QYR-APR-4D.2, QYR-APR-1B, QYR-APR-2B.1, QYR-APR-2B.2, QYR-APR-3D, QYR-APR-4D.1, and QYR-APR-4D.2) for YR APR and four QTLs (QLR-APR-4A, QLR-APR-2B, QLR-APR-3B, and QLR-APR-5A.2) for LR APR were identified. In silico analysis revealed that the key putative candidate genes such as Cytochrome P450, Protein kinase-like domain superfamily, Zinc-binding ribosomal protein, SANT/Myb domain, WRKY transcription factor, Nucleotide-sugar transporter, and NAC domain superfamily were in the QTL regions and involved in the regulation of host response towards the pathogen infection. The stable QTLs identified in this study are useful for developing rust-resistant varieties through marker-assisted selection (MAS).