Sphaerulina musiva, the causal agent of Septoria leaf spot and stem canker, is responsible for mortality and yield loss in Populus plantations. Little is known about the mode of infection and the mechanisms of resistance in this pathosystem. To characterize these phenomena, microscopic, biochemical, and transcriptome comparisons were performed between leaves of moderately resistant and susceptible genotypes of Populus inoculated with S. musiva conidia. Using scanning electron, cryofracture and laser-scanning confocal microscopy, the infection and colonization of Populus leaves by S. musiva was examined across five time points (48 h, 96 h, 1 week, 2 weeks, and 3 weeks). The infection process was similar regardless of host genotype. Differences in host colonization between susceptible and moderately resistant genotypes were apparent by 1 week post-inoculation. However, the germination of conidia was greater on the susceptible than the moderately resistant genotype (P<0.008). Diaminobenzidine staining, a measure of hydrogen peroxide accumulation, was different (P<0.001) between the host genotypes by 2 weeks post-inoculation. Transcriptome differences between genotypes indicated that the speed and amplitude of the defense response was faster and more extensive in the moderately resistant genotype. The changes in gene expression support the microscopic and biochemical observations.