The ecological and evolutionary dynamics of populations vary at different spatial and temporal scales. This is especially evident in the case of reef fishes, with bi-partite life cycles where the adult stage is benthic and sedentary, while its larval stage is capable of traveling long distances in the plankton. Understanding the genetics of populations at different evolutionary and ecological scales can help reveal metapopulation dynamics and speciation in the sea. Here I investigate population genomic patterns of the reef fish Dascyllus trimaculatus within a biogeographic province (the Red Sea and Arabian Peninsula), within an ocean basin (the Indian Ocean, that includes two biogeographic provinces), and at the intersection of biogeographic regional boundaries (at Cocos-Keeling Islands and Christmas Island, where Indian and Pacific Ocean marine faunas overlap). The goal is to understand the past and contemporary patterns of dispersal, and explore how relevant small and large-scale processes are to population subdivision and speciation. I used Restriction Site Associated DNA (RAD) markers to generate SNPs to study population genetic structure. In Chapter 1, I found strong genetic differentiation within the Red Sea. The region of Aqaba and the Northern Red Sea are different from the Central Red Sea and there is a genetic break between the Central Red Sea and the Farasan Islands. I also found differences between the Red Sea and the Arabian Peninsula populations. Most of the genetic structure was found in the loci outliers, suggesting that divergent selection may be acting on the species and allowing it to adapt to different environmental conditions. In Chapter 2, I found genetic differentiation of D. trimaculatus populations between the Nortwestern Indian Ocean biogeographic province (Red Sea and Arabian Peninsula) and the Western Indian Ocean province (Indian Ocean islands and the African coastline), supported by analysis with neutral loci and outliers. The differences between provinces may be attributed to the complex history of the Red Sea and Arabian Peninsula, the lack of suitable habitat on the coasts of Oman and Somalia, strong upwellings and the changing environmental conditions found in the Red Sea and Arabian Peninsula. The Indian Ocean D. trimaculatus has strong genetic differences with the Pacific Ocean populations. In Chapter 3, I studied D. trimaculatus populations of Pacific and Indian Ocean genetic clades in islands where the two groups overlap. I found cryptic hybridization between the Indian Ocean and Pacific Ocean D. trimaculatus genetic clades in the marine suture zone of Cocos-Keeling Islands and Christmas Island. I also found that there are consistent differences between the Pacific and Indian Ocean clades in the color of the rear of the dorsal fin. Future work will separate the Pacific and Indian Ocean D. trimaculatus into two species. This body of work shows the powerful approach of SNP markers to detect cryptic patterns of population structure, which remain difficult to discover using traditional genetic markers.