The Assay for Transposase Accessible Chromatin (ATAC-Seq) is a method for mapping genome-wide chromatin accessibility. Coupled with high throughput sequencing it enables integrative epigenomics analyses. ATAC-Seq requires direct access to cell nuclei, a major challenge in non-model species such as small invertebrates, which soft tissue is surrounded by a protective exoskeleton. Here, we present modifications of the ATAC-Seq protocol for applications in small crustaceans, extending applications to non-model species.