Cannabis is one of the oldest cultivated plants. Cannabinoids, such as cannabidiolic acid and a diversity of other secondary metabolites are produced and stored in the glandular trichomes (GTs) of female plants. However, little is known about the epigenetic mechanisms controlling the biosynthesis of these metabolites. A better understanding of these mechanisms would allow for a more optimized and tailored production of cannabinoids, terpenes and flavonoids in cannabis. Consequently, we sought out to investigate the epigenetic regulation of gene expression in four distinct tissues (glandular trichomes, leaves, stems and roots) of hemp, as an exemplar, using a combined approach of ATAC-seq and RNA-seq. We employed ATAC-seq to comprehensively map accessible chromatin regions (ACRs) across these tissues. Integration with RNA-seq data allowed us to identify tissue-specific genes and transcription factors that were associated with these ACRs. Notably, we identified ACRs that were unique to each tissue type. In the case of GTs, a portion of these tissue-specific ACRs were located within the promoter region of genes involved in the production of key secondary metabolites, offering valuable insight into the highly specialised function of GTs. Overall, our study provides a valuable resource for dissecting the epigenetic basis of tissue-specific development and secondary metabolism in cannabis. The ACRs and associated genes identified offer promising avenues for further exploration, paving the way for targeted manipulation to enhance secondary metabolite production in this important crop.