Cultural ecosystem services (CES) include the aesthetic, artistic, educational, spiritual and/or scientific values of ecosystems and have been described as ‘intangible’ and complex, reflecting diverse people-nature interactions that are embedded in dynamic linked social-ecological systems. CES have proved difficult to value, therefore mapping CES has largely concentrated on more tangible aspects, such as tourism and recreation—presenting the risk that highly significant cultural relationships, such as those between Indigenous peoples and their traditional land, will be rendered invisible in ecosystem assessments. We present our results from co-research with a group of ‘Rainforest Aboriginal peoples׳ from the Wet Tropics, Australia that illustrates a method to address this gap through mapping their perceptions of the health of Indigenous CES. We found that categories associated with biocultural diversity and governance matched their perceptions better than the usual framework that recognizes aesthetic, spiritual and other categories. Co-produced maps presented demonstrate spatial patterns of CES that are related primarily to variations in social attributes (such as adherence to cultural protocols), rather than the ecological attributes (such as biodiversity patterns). Further application of these concepts of biocultural diversity governance, and variation in social attributes when mapping CES, particularly in partnerships with Indigenous peoples is recommended.