This work is intended as a reference document to serve management at the National Oceanic and Atmospheric Administration (NOAA) and the Institute of Marine Research of Norway (IMR), with the goal of harnessing interagency collaboration to delineate a path forward for environmental DNA (hereafter “eDNA”) practical applications during the next three-to-five years (2020–25). Applications for eDNA are wide-ranging (e.g., Thomsen et al. 2016, Cowart et al. 2018, Parsons et al. 2018, Cordier et al. 2019, Ruppert et al. 2019, Salter et al. 2019, Siegenthaler et al. 2019, Djurhuus et al. 2020). This working group is specifically focused on one of the most ambitious uses, namely, eDNA for fisheries stock assessments and management. This application would create great value for commercial fisheries due to its potential cost–benefit balance. Accommodating both scientific and legislative obligations for an ecosystem-based approach to fisheries management (Link 2002, Pew Oceans Commission 2003, Pikitch et al. 2004, USCOP 2004, Link 2010, Link et al. 2011, Long et al. 2015, Huse et al. 2018), we aim to provide input not only as to how eDNA can provide supplementary data for stock assessments, but also as to how the eDNA framework can be used to support further development of EBFM. While we note that new knowledge provided by eDNA is also highly relevant for governance of marine ecosystem services in general, we restrict this paper to issues relevant for commercial fisheries management in the interest of focus and clarity. As the pace of change within the field of eDNA is so rapid, this white paper is representative of the date of publication only and should be updated in the future as demand requires. Our desire is to work in conjunction with ongoing fisheries stock assessment activities in order to enhance the applicability of eDNA-based tools, ensure their relevance and utility, address stock assessor uncertainty, and promote ongoing dialogue for appropriate prioritization of research efforts and resources.