The process of ecological speciation involves the divergence single populations into distinct species through ecologically based divergent selection. I studied the interacting developmental, genetic, and ecological mechanisms that underlie ecological speciation in populations of Icelandic Arctic charr (Salvelinus alpinus) that vary in phenotypic divergence. Arctic charr diverged into benthic and pelagic resource-based morphs after recolonization of post-glacial lakes within the last 10,000 years from a single glacial refugium. First, I assessed the role of allometric covariation between body shape and size as a source of developmental bias. I found evidence for a common pattern of phenotypic divergence across a benthic-pelagic ecological axis, which is strongly shaped by allometric effects that may facilitate rapid evolutionary responses to selection. Second, I assessed whether the requirements for adaptive divergence as the result of ecological opportunity by testing for relationships among body shape and size, resource use, and gene flow. Significant relationships between resource use and body shape and size are consistent with the existence of performance trade-offs between benthic and pelagic environments. Benthic and pelagic morphs across populations showed similar differences in resource use likely arising from a common utilization of niche space. Resource use predicted benthic and pelagic ancestry suggesting a causal link between divergence in resource use and reductions in gene flow between morphs. Lastly, I investigated the genomic consequences of adaptive divergence between sympatric morphs and reconstructed the divergence history of populations to interpret the causes of genomic patterns. Models of sympatric divergence with continuous gene flow and allopatric divergence followed by secondary contact were both supported indicating that the evolutionary history of this species is more complex than originally thought. Phenotypic and ecological variation was associated with genomic differentiation between sympatric morphs and the formation of many narrow genomic regions of differentiation, which are related to both phenotypic and ecological variation in divergent populations. This suggests that divergent selection has resulted in the genomic differentiation of sympatric morphs. Overall, my study suggests that adaptive divergence in response to environmental heterogeneity promotes parallel phenotypic specialization on resources which may lead to genomic differentiation and ultimately ecological speciation with gene flow.