AbstractNatural dietary shifts offer the opportunity to address the nutritional physiological characters required to thrive on a particular diet. Here, we studied the nutritional physiology of Podarcis siculus, with populations on Pod Mrčaru, Croatia, that have become omnivorous and morphologically distinct (including the development of valves in the hindgut) from their insectivorous source population on Pod Kopište. We compared gut structure and function between the two island populations of this lizard species and contrasted them with an insectivorous mainland out-group population in Zagreb. On the basis of the adaptive modulation hypothesis, we predicted changes in gut size and structure, digestive enzyme activities, microbial fermentation products (short-chain fatty acids [SCFAs]), and plant material digestibility concomitant with this dietary change. The Pod Mrčaru population had heavier guts than the mainland population, but there were no other differences in gut structure. Most of the enzymatic differences we detected were between the island populations and the out-group population. The Pod Mrčaru lizards had higher amylase and trehalase activities in their hindguts compared with the Pod Kopište population, and the Pod Kopište lizards had greater SCFA concentrations in their hindguts than the omnivorous Pod Mrčaru population. Interestingly, the differences between the Pod Mrčaru and Pod Kopište populations are primarily localized to the hindgut and are likely influenced by microbial communities and a higher food intake by the Pod Mrčaru lizards. Although subtle, the changes in hindgut digestive physiology impact the digestibility of plant material in adult lizards-Pod Mrčaru lizards had higher digestibility of herbivorous and omnivorous diets fed over several weeks in the laboratory than did their source population.