Next-generation sequencing (NGS) based genomic studies are revolutionizing the field of wildlife biology. These methods have yielded unprecedented insights for understanding ecology, evolution and conservation of wild populations. Despite the advantages, biodiversity rich regions in the tropics need more NGS-based studies to understand their native species. However, the field has progressed very slowly in these regions due to several challenges, including that most experts in the field are not based here. In this article, we highlight the factors that need to be considered before initiating a wildlife genomics research project with a focus on south and south-east Asia, though several factors apply to other regions as well. We highlight the challenges like policy issues for collecting samples and need for better sequencing and computational infrastructure. Finally, we discuss how global initiatives can help such regions setup NGS-based studies of wildlife.