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Our planet finds itself in the sixth extinction crisis, this one being of an anthropogenic nature. In the NGS era, evolutionary biologists now have an opportunity to contribute to conservation with the help of genome wide data. In this presentation, I provide an overview of a number of Southeast Asian case studies in which the application of NGS based methodologies has contributed directly to species conservation and survival, including: (1) population-genomic assistance in ex-situ breeding of terminally endangered vertebrates; (2) detection of introgressive hybridization and genomic infiltration of foreign alleles in depleted populations; (3) inference of origin of traded individuals; and (4) discovery of significant cryptic diversity in an understudied fauna. Southeast Asia is one of the richest and – at the same time – one of the most anthropogenically impacted regions in the world, and shows the strongest beginnings of the impending extinction crisis. Conservation-genomics offers an increasingly affordable remedy for the lack of pertinent information on what to save and how to save it.