Although it is commonly assumed that most speciation occurs in allopatry, a growing body of research indicates that natural selection can lead to reproductive isolation and speciation in sympatry. A common mechanism for sympatric speciation is ecological speciation, where diversification is driven by differential selection across ecological niches. New genetic and genomic techniques facilitate the discovery of cryptic ecological divergence, and allow us to examine in detail the relative roles of natural selection and gene flow in speciation, particularly in marine systems, where it is difficult to identify mechanisms for allopatric speciation. This dissertation combines broad exploratory field sampling with population genetic and phylogenetic methods to tease apart the roles of geographic isolation and natural selection in driving speciation in the Coral Triangle. Using the coral-associated nudibranch genus Phestilla as a model, in chapter 1 we examine the effect of coral host and geography on population divergence in Phestilla lugubris and Phestilla minor. Phylogenetic analyses and analyses of molecular variance of mitochondrial COI sequences indicate very little population structure in Phestilla lugubris, but Phestilla minor has diverged across the Sunda Shelf and across two major clades of coral host. In chapter 2 we use population genomics to test whether natural selection plays a larger role in the divergence of sympatric host-separated populations than allopatric populations of Phestilla minor. Population genetic analyses of genome-wide single nucleotide polymorphisms show host-driven divergence is stronger than that across the Sunda Shelf, despite having occurred more recently. Genomic scans for selection reveal an important role for natural selection in both geographic and host-associated divergence. Finally, in chapter 3 we broadened our approach to examine the roles of geography and host in diversification of all scleractinian-associated nudibranchs. A phylogenetic tree of COI, 16S, and H3 sequences from scleractinian-associated nudibranchs collected across the Indo-Pacific Ocean reveals three times the number of purported species than previously thought, with evidence for host shifting and geographic divergence multiple times throughout evolutionary history. Combined, these three studies demonstrate that both coral host and geography contribute to diversification both within and between species of scleractinian coral-associated nudibranchs.