Due to its ability to spread quickly and result in tree mortality,Sphaerulina musiva (Septoria)is one of the most severe diseases impactingPopulus. Previous studies have identified thatSeptoriainfection induces differential expression of phenylpropanoid biosynthesis genes. However, more extensive characterization of changes to lignin in response toSeptoriainfection is lacking. To study the changes of lignin due toSeptoriainfection, four field grown, naturally variantPopulus trichocarpaexhibiting visible signs ofSeptoriainfection were sampled at health, infected, and reaction zone regions for cell wall characterization. Fourier transform infrared spectroscopy (FTIR), nuclear magnetic resonance (NMR), and acid hydrolysis were applied to identify changes to the cell wall, and especially lignin. FTIR and subsequent principal component analysis revealed that infected and reaction zone regions were similar and could be distinguished from the non-infected (healthy) region. NMR results indicated the general trend that infected region had a higher syringyl:guaiacyl ratio and lowerp-hydroxybenzoate content than the healthy regions from the same genotype. Finally, Klason lignin content in the infected and/or reaction zone regions was shown to be higher than healthy region, which is consistent with previous observations of periderm development and metabolite profiling. These results provide insights on the response ofPopuluswood characteristics toSeptoriainfection, especially between healthy and infected region within the same genotype.