This thesis aims to contribute to the modernization of Canada’s national rose breeding program by developing molecular markers associated with traits of major interest. Roses are one of the most economically important ornamental crops. Consumers’ preferences are continuously evolving, meaning that the rose industry needs to release new varieties at a fast pace to remain competitive. As a consensus, consumers want low maintenance roses. To meet consumers’ demand, Canada’s national rose breeding program, which is hosted in the Niagara Region, focuses on breeding for black spot disease resistance and winter hardiness. In this regard, Canadian Explorer roses are known worldwide for their exceptional hardiness. The objective of this thesis was to identify quantitative trait loci (QTL) associated with resistance to black spot disease (Diplocarpon rosae) and winter hardiness in polyploid bi-parental populations derived from Explorer roses, and to set up a framework for the development of molecular markers and the implementation of marker-assisted selection. Molecular tools not only have the potential to improve the accuracy and speed of the selection process, but they also promise to reduce the cost and the labor associated with recording complex phenotypic traits. This research identified a major QTL associated with the resistance to several races of Diplocarpon rosae under natural and artificial conditions on linkage group 1 of the rose genome for which a diagnostic marker was designed and validated in the genetic background of the parental donor. Furthermore, this research identified several QTLs associated with winter damage, spring regrowth and freezing tolerance measured by electrolyte leakage in artificial conditions. While no diagnostic markers were developed, this research highlighted the limited utility of electrolyte leakage as a proxy for field winter hardiness and the complexity of this phenotypic trait. Together, these results demonstrate the potential for implementing marker-assisted selection for black spot disease resistance in a rose breeding program, and provide a starting point for the molecular characterization of the genetic and molecular basis of winter hardiness in roses.