Indigenous peoples and indigenous knowledge systems are now considered as vital components of global conservation, science-policy assessments, and global targets indicated in the UN 2030 Agenda. In this Ph.D. project, I critically reviewed the social, political, and environmental issues over the concept of “indigenous peoples” in Asia and its implications for local and international policies with emphasis on the UN Sustainable Development Goals (SDGs) of the 2030 Agenda. This study showed that the legitimate recognition of indigenous peoples and indigenous knowledge systems and practices (IKSP) are important to achieve the SDGs. Zero Hunger (SDG 2), for example, may be achieved through the valorisation and conservation of the indigenous food system, biocultural refugia, and local plant resources. The food ethnobotany of the Higaonon tribe of Bukidnon in the Philippines provided valuable insights on the potential of neglected and underutilised species (NUS) in the diversification of the nutrient-poor and rice-centred diet of the majority of the Filipinos. The Higaonon tribe’s local staples consisted of yautia, taro, sweet potato, maize, and other NUS, may be tapped as additional food and nutrient sources to address the country’s problem of malnutrition and micronutrient deficiencies. This Ph.D. project also demonstrated the benefits of collaboration with indigenous peoples in the co-production of knowledge, specifically on improving food safety in the local communities. Using the Two-Eyed Seeing approach, the protocol for the molecular identification of a poisonous wild yam locally known as ‘Lab-o’ (Dioscorea hispida Dennst.) was developed along with documentation of the traditional detoxification process practised by the Higaonon tribe. Apart from its function as a reservoir of ethnobotanical knowledge, indigenous traditional territory is also home to a new species of Begonia L., a member of a horticulturally valuable group of flowering plants. Named after the Bangsamoro people of the southern Philippines, Begonia bangsamoro reflects the name and cultural identity of both the people and the land, and implicitly acknowledges indigenous relationships with the environment. This culture-sensitive approach in taxonomic naming contributed to the societal recognition of the indigenous peoples’ rights, and it also opened the opportunity for a meaningful engagement with the indigenous peoples and the government for conservation. Lastly, my Ph.D. thesis redefined the research approach in the field of taxonomy and ethnobotany to be socially just in a way that respects the universal rights of indigenous peoples, their land, and resources.