Adopting a new diet is a significant evolutionary change and can profoundly affect an animal's physiology, biochemistry, ecology, and its genome. To study this evolutionary transition, we investigated the physiology and genomics of digestion of a derived herbivorous fish, the monkeyface prickleback (Cebidichthys violaceus). We sequenced and assembled its genome and digestive transcriptome and revealed the molecular changes related to important dietary enzymes, finding abundant evidence for adaptation at the molecular level. In this species, two gene families experienced expansion in copy number and adaptive amino acid substitutions. These families, amylase, and bile salt activated lipase, are involved digestion of carbohydrates and lipids, respectively. Both show elevated levels of gene expression and increased enzyme activity. Because carbohydrates are abundant in the prickleback's diet and lipids are rare, these findings suggest that such dietary specialization involves both exploiting abundant resources and scavenging rare ones, especially essential nutrients, like essential fatty acids. Main Populations exposed to new environments often experience strong natural selection (e.g., Herrel et al. 2008). Comparing closely related species has been an effective perspective in pinpointing changes that drive adaptation (Dasmahapatra et al. 2012; Lamichhaney et al. 2015). In its most powerful incarnation, the comparative method links variation at the genetic level to molecular phenotypes that in turn change how whole organisms interact with their environments, revealing for example adaptation to new abiotic factors (Protas et al. 2006; Chakraborty and Fry 2015; Peichel and Marques 2017; Tong et al. 2017; Chen et al. 2018), changes in diet (Harris and Munshi-South 2017; Hsieh et al. 2017; Zepeda-Mendoza et al. 2018), and exposure to pollution (Vega-Retter et al. 2018). In animals, digestion is an ideal model phenotype because it is central to fitness, is understood in many species at genetic, molecular, biochemical, and physiological levels, and is a trait that shows abundant variation throughout animal evolution (Karasov and Martinez del Rio 2007). While studies of animal digestion have yielded insights into the physiology and biochemistry of adaptation, untangling its genetic basis is contingent on the availability and quality of genomic resources, which have traditionally been lacking in nonmodel species. Advances in genome technology have improved the quality and decreased the cost of obtaining sequences, stimulating the production of genome assemblies and catalyzing genetic discoveries for a diverse array of non-model organisms.Here we describe the genetic changes accompanying acquisition of an herbivorous diet in the marine intertidal fish, Cebidichthys violaceus. To do this we generated a physiological genomics dataset for this non-model species, including a highly contiguous and complete genome, the transcriptomes of digestive and hepatic tissues, and digestive enzyme activity levels.