Faba bean is gaining attention in Australia as a rotation grain legume where most of the country’s produce is exported. Rust, caused by Uromyces viciae-fabae, is a major constraint to Faba bean production in eastern Australia and its chemical control results in increased cost of production. The deployment of diverse sources of resistance in new cultivars underpins economic and eco-friendly control of rust diseases of crops. A selection from cultivar Doza (Doza#12034) and a European accession Ac1655 exhibited seedling rust resistance against U. viciae-fabae pathotype 24–40. Doza#12034 and Ac1655 were crossed with a susceptible genotype Fiord and recombinant inbred line (RIL) F₆ populations were generated. Rust tests on Fiord/Doza#12034 and Fiord/Ac1655 F₄ and F₆ populations demonstrated monogenic inheritance of resistance in both crosses and the underlying resistance loci were named Uvf-2 and Uvf-3, respectively. Genetic mapping of both RIL populations located Uvf-2 and Uvf-3 in chromosomes III and V, respectively. The SNPs that showed linkage with Uvf-2 and Uvf-3 were converted into kompititive allele specific PCR (KASP) assays. Markers KASP_Vf_0703 and KASP_C250539 flanked Uvf-2 at 4.9 cM and 2.9 cM distances, whereas Uvf-3 was flanked by KASP_Ac×F165 (2.5 cM) and KASP_vf_1090 (10.1 cM). Markers KASP_Vf_0703 and KASP_Ac×F165 can be used for marker-assisted selection of Uvf-2 and Uvf-3, respectively, after confirming parental polymorphisms.