Melampsora willow rust, caused by Melampsora spp., is a devastating foliar disease of willow in much of the world. These pathogens colonize willow leaf tissue, form uredinial pustules, and rapidly asexually reproduce. Despite their prolific and devastating life cycles, little is known about these pathogens in New York State. In order to gain an understanding of these rusts on Salix purpurea, I collected isolates from New York and surrounding states for five years to use in population biology studies as well as host resistance assays. Through this work, I was able to identify the two primary species infecting S. purpurea as M. americana and M. paradoxa. Select host genotypes were inoculated with a subset of rust isolates to characterize their potential as breeding families for mapping host resistance. This work led an eQTL mapping project in a single S. purpurea breeding family segregating for rust resistance to map regions of the genome associated with differential expression of host transcripts important in conferring resistance. On the pathogen side, the eQTL project identified two candidate fungal effectors that may play roles in M. americana pathogenicity. Population biology studies conducted on both M. americana and M. paradoxa revealed that M. americana was highly diverse across all regions assayed whereas M. paradoxa was isolated from only one location and all isolates were clonal. Since the M. paradoxa clonal lineage was collected from the same field in multiple growing seasons, I hypothesized that the pathogen is overwintering in willow stem cankers. This provides information on the expected life cycles of the two most important rust species on S. purpurea in New York and can guide breeding strategies to combat these pathogens.