This study focuses on describing the distribution of histone modifications in the model system for woody perennial trees, Populus.tremula x alba 717-1B4. We examined three histone modifications, H3K36me3, H3K4me3 and H3K27me3. Our results suggest that the distribution of these modifications is very similar to that of Arabidopsis thaliana. All three modifications are enriched on euchromatic chromosome arms within genes rather than the heterochromatic centromere region. While H3K36me3 and H3K4me3 are enriched on the most highly expressed genes, H3K27me3 is enriched on genes that have the lowest expression levels. Additionally, we identified differentially methylated H3K27me3 genes in Populus.tremula x alba 717-1B4 and Arabidopsis thaliana. The results of this study have helped us understand that histone modifications distribution and function are conserved in both annual and perennial plant species.