One general approach for assessing whether phenotypic variation is due to selection is to test its correlation with presumably neutral molecular variation. Neutral variation is determined by population history, the most likely alternative explanation of spatial genetic structure, whereas phenotypic variation may be influenced by the spatial pattern of selection pressure. Several methods for comparing the spatial apportionment of molecular and morphological variation have been used. Here, we present an analysis of variance framework that compares the magnitudes of latitudinal effects for molecular and morphological variation along a body size cline in Australian Drosophila populations. Explicit incorporation of the relevant environmental gradient can result in a simple and powerful test of selection. For the Australian cline, our analysis provides strong internal evidence that the cline is due to selection.