Himalaya and the Tibetan Plateau, known as the ‘land of snow’ and the ‘roof of the world’, is home to tens of millions of indigenous people who live with a staggering amount of biological diversity. In the past decade scientists have applied genomic tools and methods to substantially advance the understanding of phylogeography and genetic mechanisms behind high-elevation adaptation of local biota. However, contributions from indigenous researchers and native institutions are underrepresented in this scientific endeavour. We point to the higher degree of indigenous contribution within the discipline of conservation biology and how recognizing the prominence of traditional ecological knowledge (TEK) could deliver keen molecular ecological insights. Since the Himalaya-Tibet ecological interface spans five countries, comprehensive biogeographical and phylogeographical taxon sampling in the region requires multi-national collaborations across indigenous lands as well as indigenous community participation at both national and international levels. For the next generation of indigenous molecular ecologists, researching and cataloguing the evolutionary history and genetic information of the Tibetan and Himalayan landscape is a race against the melting glacier. At the roof of the world, their scientific judgement and stewardship will have environmental impacts that percolate far beyond indigenous lands.