This document sets out key recommendations for monitoring threatened species populations. Species-specific recommendations are provided for 25 species (six birds, three frogs, nine mammals, two reptiles and five plants). These species-specific recommendations identify best-practice methods based on the recommendations of the species experts, which are based on successful monitoring methods conducted in the past (enabling comparisons) and what current best-practices are considered most suitable. Over time, as technologies improve and innovative techniques evolve, the best-practice methods will likely be updated. In addition to the species-specific recommendations outlined, general information is provided that can be applied to monitoring all species, regardless of conservation status. If utilising modules of the Ecological Monitoring System of Australia (EMSA), and especially if using the associated EMSA app Monitor, the general recommendations are already built into the design, workflows, and standards of EMSA.