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We report the results of a population-genetic study of the short-nosed fruit bat, Cynopterus sphinx (Pteropodidae). The purpose of our study was to assess the relative importance of drift, gene flow, and spatially varying selection in shaping patterns of genetic and phenotypic variation across a latitudinal climatic gradient in peninsular India. At a microgeographic scale, polygynous mating resulted in a substantial reduction of effective population size. However, at a macrogeographic scale, rates of migration were sufficiently high to prevent a pronounced degree of stochastic differentiation via drift. Spatial analysis of genetic and phenotypic differentiation revealed that clinal variation in body size of C. sphinx cannot be explained by a neutral model of isolation by distance. The geographic patterning of morphometric variation is most likely attributable to spatially varying selection and/or the direct influence of latitudinally ordered environmental effects. The combined analysis of genetic and phenotypic variation indicates that recognized subspecies of C. sphinx in peninsular India represent arbitrary subdivisions of a continuous spectrum of clinal size variation.