Abstract The bringing together of multiple knowledge sources, such as Indigenous knowledge (IK) and Environmental science Knowledge (ESK), is a topic of considerable interest and significance in environmental research. In the areas of resource management for example, the bringing together of IK and ESK datasets has raised considerable interest for its potential to increase understanding and provide insights into complex phenomena such as the effects of climate change and variability on wildlife health and distribution. The potential benefits that exist from merging these knowledge sources have been widely acknowledged. However, navigating the complex processes involved in knowledge linking continues to pose significant challenges. This systematic mapping protocol will guide the collection and analysis of literature to examine the approaches and methods used in published studies that aim to bring together Indigenous and Environmental science Knowledge in environmental research. The particular focus of this examination is placed on identification of the types of approaches and methods used to merge IK and ESK datasets at the stages of data analysis, results, and interpretation/discussion in the research process. Through a scoping exercise, a draft search string was developed based on a predetermined list of keywords. Consultation was held with a senior Indigenous scholar to advise on the keywords used and consideration for IK likely to be represented in the collected literature. The final search string will be applied to online bibliographic databases to collect studies published in peer‐reviewed journals. The final capture of the search will be screened in two stages: (1) at the level of title and abstract and (2) at full‐text. All studies included will be coded using a standardised coding template and a narrative synthesis approach will be used to identify patterns in the evidence, including knowledge gaps and clusters. Practical implication: The resulting systematic map, following the outlined procedures in this protocol and considering guidelines from the Collaboration for Environmental Evidence (CEE) and Reporting standards for Systematic Evidence Syntheses (ROSES), can serve to support and inform future research endeavours engaged in working towards the linking of IK and ESK, with practical implications for communities and policymakers.