We describe here a step-by-step protocol for the generation of sequence-ready libraries for the Assay for Transposase Accessible Chromatin (ATAC-seq) that provides a positive display of accessible, presumably euchromatic regions. The protocol is straightforward and can be used with small individuals such as daphnia and schistosome worms, and probably many other biological samples of comparable size. This makes the method suitable for population epigenomics studies. This protocol is based on the protocol from Corces et al. (2016), Buenrostro et al. (2015) and Nextera DNA Library Prep Kit (2017) with some modifications. Controls must be done without organisms as input.