Like any other country in the tropical and subtropical regions, wild yams are considered an important food by many indigenous peoples in the Philippines and other parts of Southeast Asia. Yet, cases of intoxication and even death have been reported due to wild yam consumption. Unfortunately, some locals cannot differentiate the edible from the poisonous species that require further processing whilst ethnobotanical information remains scarce. In this study, we determined the identity of a poisonous wild yam locally known as “Lab-o” to the Higaonon tribe of Bukidnon province in the Mindanao island, Philippines. Due to highly diverse morphological variations within species and varieties of yams, “Lab-o” was identified through DNA barcoding. Based on the BLASTn analysis, the wild yam in question was identified as Dioscorea hispida Dennst. which further confirms the reported toxicity of the yam. To bridge scientific knowledge and indigenous knowledge system, we also explored the traditional processing methods of wild yam detoxification practiced by various indigenous cultures. The DNA barcoding protocol described in this study may serve as a reference to accurately identify the plant in the wild. The poisonous yams may be labelled with appropriate warnings and preparation guides as preventive information measures to avoid the incidences of poisoning and death. The indigenous knowledge and practices associated with the utilisation of Dioscorea hispida Dennst. and other neglected and underutilised plant resources could be likewise considered in addressing food safety and food insecurity in the Asian region.