The under-ground mushroom Tuber indicum is renowned for its economic, nutritional, ethnobotanical and ecological importance. For the development of sustainable harvest and conservation practices, better knowledge about the mushroom’s habitat is indispensable. However, few approaches allow monitoring T. indicum’s distribution on a large geographic scale. Apart from the difficulty to directly monitor them by Remote Sensing and GIS technology, a particular challenge arises from the sampling limitations for this seasonal mushroom. This problem is common in geology, where underground mineral resources must be mapped without direct observations. Geologists apply the ‘Weights of Evidence’ method for such situations, and this approach may have potential for underground mushrooms as well. We thus constructed potential habitat maps for T. indicum using the Weights of Evidence method. Based on field survey and published sources, ten influential indicators associated with T. indicum were selected and mapped for Longyang district in southwestern Yunnan, China. Two predictive models were established from independent environmental layers. In order to build better understanding of the models’ predictive ability, apart from the Receiver Operating Characteristic (ROC) curve, the Area Adjusted Frequency (AAF) approach was also applied for model evaluation. For the final map, the best-performing model was selected. The resulting habitat map could provide guidance for future conservation activities.