The Saving our Species (SoS) program is an initiative of the NSW Department of Planning, Industry and Environment, aimed at ensuring the viability of as many threatened species in the wild as possible for the next 100 years. The practical side of the SoS program is the development and implementation of conservation projects and interventions for a wide range of threatened species. To facilitate the evaluation of these projects, the Department has developed a monitoring, evaluation and reporting (MER) framework for managed species. The framework states the key evaluation question for all SoS conservation projects as: ‘Is the species, habitat or threat responding to management as expected, regarding a particular site or population?’. These guidelines expand on the monitoring, evaluation and reporting (MER) framework by providing NSW Government's SoS project coordinators with a step by step approach to using conceptual models for selecting relevant indicators and estimating a species’ expected response to management for these indicators.