The Anolis lizards are a well-known example of an adaptive radiation, but the evolution of one of their most characteristic features, the dewlap, remains somewhat of a mystery. The dewlap is an extendable throat-fan, which is used for sexual displays and visual communication. Across the genus there is spectacular variation in colour, pattern and size of the dewlap, but our understanding of how this variation contributes to population divergence and speciation is limited. To address this gap, I have leveraged a discrete colour-pattern polymorphism in a Panamanian Anolis lizard, with mate choice experiments, lab crosses, RAD-tag sequencing and environmental data to investigate the evolution and maintenance of this colour polymorphism. I have determined that dewlap colour-pattern is a mendelian trait. The distribution of colour-pattern morphs is related to an environmental gradient, consistent with what we predict based on signalling theory: darker dewlaps in drier environments, and individuals with a different dewlap colour-pattern vary in life history characteristics, including growth and reproductive rate. I also found evidence of incomplete reproductive isolation between morphs and populations, in the form of colour assortative mating and reduced fitness of F1 hybrids. Using genome-wide SNP data I have estimated genetic differentiation between these populations and found that this was related to the environmental gradient and phenotypic divergence. Between populations geneflow was high, but several loci were found to be strongly associated with the environmental gradient and will be interesting candidate loci for future work. This study represents a comprehensive body of work detailing the relationships between environmental, phenotypic and genetic variation in this colour polymorphic species. The results suggest that ecologically driven divergence in dewlap colour-pattern is contributing to reproductive isolation and population divergence.