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One hundred and fifty years after Darwin and “On the Origin of Species,” understanding how phenotypic variation is generated, maintained, and lost remains a central goal in evolutionary biology. Color polymorphic species are model systems for examining phenotypic variation in nature because discrete color variants are phenotypic markers of underlying genetic variation, or allele frequencies. Color polymorphism is the presence of multiple discrete, heritable color phenotypes within a single breeding population. Color morphs have evolved in thousands of species across the plant and animal kingdoms. Lizards have repeatedly evolved strikingly similar color polymorphisms in distantly related lineages, providing an opportunity to examine the effects of heritable phenotypic variation on micro- and macroevolutionary dynamics, intraspecific geographic variation, correlated traits, and associated evolutionary processes.Herein, I take an interdisciplinary approach to understand the causes and consequences of color polymorphism at multiple biological scales, from molecules to macroevolution. In Chapter 1, I studied hundreds of individuals within a single population of lizards (Aegean wall lizard, Podarcis erhardii) to characterize a previously undescribed color polymorphism and identify color morph-correlated traits important for lizard fitness. I found that P. erhardii has three pure color morphs (orange, yellow, and white), and that male morphs display significant differences in body size traits, bite force, and chemical signal profiles extracted from their femoral pore exudate, whereas female morphs do not differ in head and body size dimensions or their maximum bite force capacity. I expand on these differences in traits in Chapter 2, where I conducted behavioral experiments on male P. erhardii color morphs from the same population to elucidate morph differences in behavior. Laboratory experiments revealed that male color morphs differ in their ability to access a limited space resource, and exhibit different levels of aggressive, bold, and signaling behaviors depending on the color morph identity of their competitor. In Chapter 3, I sampled lizards and measured environmental variation from 46 island populations across the range of P. erhardii to reconstruct the evolutionary history of color polymorphism and identify morph-environmental associations. I found that color polymorphism is likely the ancestral state of P. erhardii, and that morph variation is likely due to morph loss, which occurs at a much faster rate than evolutionary gains of color polymorphism. I also found that morph diversity seems to be lost in an ordered fashion, and that the rare orange morph is associated with cooler, wetter habitats, which are disappearing with climate change. Finally, in Chapter 4, I demonstrate that color polymorphism is a driver of diversification in the lizard family Lacertidae. Taken together, my dissertation suggests that the causes of color polymorphism is variation in the environment, and the consequences are variation within species that lead to the generation of new species.