Although divergence in expression is thought to be a hallmark of functional dispersal between paralogs postduplication, there is currently a limited understanding of the mechanisms underlying the necessary transcriptional alterations as recent studies have suggested that only a very small proportion of expression variation could be explained by transcriptional variation between paralogs. To further this understanding, we examined comprehensively curated regulatory interactions and genomewide nucleosome occupancy in budding yeast to specifically determine the contribution of cis-elements to expression divergence between extant duplicates. We found that divergence in activation by transcription factors plays a more important role in expression divergence of paralogs than previously appreciated; further, analysis of promoter chromatin structure demonstrated that differential nucleosome organization is coupled with divergent expression of paralogs. By incorporating information of cis-elements encoding transcriptional regulation and chromatin structure, we improved the fraction of expression variation that was previously shown to be explained based on known cis-transcriptional effects by approximately 3-fold. Taken together, our analysis highlights the importance of chromatin divergence involved in expression evolution between paralogs.