Crown rust caused by Puccinia coronata f.sp. avenae is the most destructive fungal disease threatening oat production worldwide. Therefore, a search for novel sources of genetic resistance is considered essential to combat the evolving races of pathogen. The objectives of this study were to develop two recombinant inbred line mapping populations carrying novel sources of crown rust resistance and identify the genomic regions associated with crown rust resistance. 108 and 112 F5:6 RILs developed from each of the bi-parental crosses were evaluated for disease incidence in field and greenhouse under randomized complete block experimental designs with two replications. Genotyping and linkage analysis of markers associated with RILs revealed a major QTL underlying disease resistance in each population respectively. The two QTL identified in this study showed consistency across all the tested locations and the markers associated with the QTL appear to be useful for marker-assisted selection in oat breeding programs.