The Coral Triangle is the global epicenter of marine biodiversity. While this pattern has been known for decades, the origins of this pattern are still actively debated. Integrating phytogeographic and genomic data with physical oceanographic modeling and ecology, we demonstrate pluralistic drivers of marine diversification in this region ranging from eustatic sea level changes to ecological divergence. We have used this research as a platform both for building capacity in one of the worlds most imperiled and least studied marine ecosystems as well as increasing diversity in marine sciences. Through the integration of education and research, we are creating future biodiversity leaders in Indonesia and diversifying marine science in the United States.