The Coral Triangle is the global epicenter of marine biodiversity. These marine resources are a critical source of jobs and food security in this region. Despite this importance, the reefs of the Coral Triangle are in decline, threatening the stability of this ecosystem and the services it provides humanity. A major obstacle to achieving sustainability in the Coral Triangle is that the size and biological diversity in this region exceeds the science capacity needed to understand its dynamics and to educate the public on its importance. A key to developing this capacity is international partnerships that leverage expertise and resources from the international scientific community with the passion and knowledge of local scientists. Results from genetic and genomic tools highlight the importance of vicariance and ecological speciation in shaping the Coral Triangle biodiversity hotspot. Importantly, by conducting this work in the context of collaborative science capacity building, this work advances our understanding of the processes generating biodiversity in the Coral Triangle while generating data and human resources that will be essential for its protection.