Assay for Transposase Accessible Chromatin followed by sequencing (ATAC-seq) is one of the widely used methods to understand the chromatin accessibility and identification of various cis-regulatory elements like enhancers, promoters, insulators, etc. in the genome. Initially proposed in animal model systems, this method has now been adopted successfully for few plant species. There is a need for further improvement with respect to sample preparation and tool development that can help users extract more precise and meaningful information to understand complex regulatory networks involved in plant growth, development, and responses to external stimuli. This book chapter aims to provide a brief overview of the preparation of the ATAC-seq libraries and various tools available to process the data.