Interpopulation variation in morphology, such as that among small island populations, plays a key role in speciation and diversification. There are two approaches to investigating evolution of morphological characters: comparing patterns of trait variances and covariances within and among populations, and testing particular adaptive scenarios. Here, we combine both approaches to infer the role of natural selection in shaping morphological variation in body size, head color pattern, and body shape among 10 populations of a day gecko, Phelsuma ornata, and its close relative, P. inexpectata, in the Mascarene Islands. We find that local populations are morphologically distinct, and that natural selection has likely influenced phenotypic diversification in the group. Lizards on small outer islands tend to be larger than lizards on the mainland of Mauritius. For body shape and head color pattern, comparisons of variation within and among populations reveal that differences among populations for some variables are too great to be explained by neutral processes alone, although we cannot identify the causal agents for this selection. These results reveal that the forces shaping different sets of organismal traits may be distinct, such that a variety of statistical approaches are needed to investigate selection in natural populations.