My research uses next generation sequencing techniques and bioinformatic tools to identify complex patterns of evolutionary adaptations within marine fishes. Modern genetic tools allow us to tease apart the vast genetic information and variation that occurs within and between species. From my Ph.D. work, I identified loci under positive Darwinian selection across multiple rockfishes (genus Sebastes) to better understand adaptation within marine habitats. Genes under positive selection belonged to a variety of gene functions which included immune function, development, growth, and oxygen transport. In addition, hemoglobin subunit α genes were identified to be under strong positive selection across multiple rockfish species, which supports the hypothesis that oxygen concentrations varying as a function of depth play a major role in the radiation of this genus. From my postdoctoral work, I sequenced the genome and the transcriptomes of nine tissues of the monkeyface prickleback, Cebidichthys violaceus (Teleostei: Stichaeidae), to gain insight into how this fish species thrives on an herbivorous diet in a heterogeneous intertidal habitat. From the C. violaceus genome, we have been able to identify copy numbers of candidate genes (i.e. amylase and bile salt activated lipase) and differential gene expression patterns to make stronger inferences about dietary specialization. Coupled with biochemical data, it is clear that C. violaceus has a ketotic metabolism due to this species’ reliance on microbial symbionts in their hindguts. This sets C. violaceus apart from other herbivores within its family. Both of these investigations provide insight on the molecular evolutionary processes within fishes to better understand physiological adaptations to marine habitats.