The rapid uptake of environmental DNA methods globally is an indication of its potential in environmental monitoring. In less than 15 years, the field of eDNA has matured well beyond the proof-of-concept state to current moves towards integration in research and monitoring projects globally. Australian and New Zealand researchers have played an important role in this eDNA revolution and as a region we continue to be at the leading edge of many new developments in the field. Despite this expertise, however, integration in official biomonitoring programs remains limited. There remains strong hesitancy with resource managers using eDNA because of the lack of a standardised biomonitoring workflow. National best practice guidelines are essential for the uptake of eDNA methods in government mandated biosecurity and ecosystem monitoring programs. As a cross-institutional group of >30 eDNA experts, we developed the first AUS/NZ best practice eDNA guidelines for monitoring programs and present the document to the wider marine science community. We aim to encourage integration of eDNA methodologies in biomonitoring, so resource managers can use the best available technologies to ensure a sustainable future for our region’s rich biodiversity.