Anolis lizards of the Greater Antilles represent one of the classic examples of vertebrate adaptive radiation. The same morphological types (‘ecomorphs’) have evolved repeatedly in response to similar ecological pressures on different islands. We tested whether patterns of within species diversification were congruent with between species patterns and the processes leading to the adaptive radiation of Greater Antillean anoles by measuring variation in performance-related morphological characters in the brown anole, Anolis sagrei. We measured morphological and genetic variation in two different habitat types on each of five islands in the Bahamas. We estimated population structure and rates of gene flow within and among islands using eight microsatellite markers. Intraspecific variation in performance-related morphological characters was similar to the pattern of interspecific variation that characterizes the adaptive radiation of this group in the Greater Antilles. For example, limb length was correlated with perch diameter within A. sagrei as has also been shown among species of anole. Morphological divergence in traits has occurred despite relatively high levels of gene flow both within and among islands. These results are discussed in the context of the divergence-with-gene-flow model of speciation. The results provide important intraspecific evidence that the diversification of anoles has been shaped by natural selection and show how ecologically-based selection pressures explain diversification at both the population and species levels. © 2007 The Linnean Society of London, Biological Journal of the Linnean Society, 2007, 90, 189–199.