Patterns of intraspecific geographic variation in morphology and behaviour, when examined in a phylogenetic context, can provide insight into the microevolutionary processes driving population divergence and ultimately speciation. In the present study, we quantified behavioural and phenotypic variation among populations from genetically divergent regions in the Central American treefrog, Dendropsophus ebraccatus. Our fine-scale population comparisons demonstrated regional divergence in body size, colour pattern frequencies, and male advertisement call. None of the characters covaried with phylogenetic history or geographic proximity among sampled populations, indicating the importance of highly localized selection pressures and genetic drift in shaping character divergence among isolated regions. The study underscores how multiple phenotypic characters can evolve independently across relatively small spatial scales. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 97, 298–313.