Dinoflagellates are a diverse group of eukaryotic microbes that range from free-living, parasitic to photosymbiotic species in a broad spectrum of trophism. Of these, the photosymbiotic taxa critically sustains the coral reefs by providing fixed carbon and essential nutrients to reef-building corals. Genomes of dinoflagellates are known to be large (some are over 200 Gbp), complex, and exhibit idiosyncratic features compared to other eukaryote genomes. Since 2018 we have generated genome data from 18 dinoflagellate taxa encompassing 13 species, largely from symbionts of corals and other coral reef organisms. In this talk, I will present results from our recent comparative analyses of whole-genome sequences of these taxa revealing extensive genomic divergence even among different isolates of the same species, highlighting phylogenetic diversity that is hidden behind subtly different morphology. Our analysis of a thermotolerant symbiotic species further revealed how whole-genome duplication has enhanced its efficiency and resilience as a coral symbiont in warming oceans. These results demonstrate the power of comparative genomics in clarifying evolutionary processes related to diversification of these eukaryotic microbes to become one of the most ecologically successful organisms.