The structure of body size and shape divergence among populations of Poecilia vivipara inhabiting quaternary lagoons in South-eastern Brazil was studied. This species is abundant throughout an environmental gradient formed by water salinity differences. The salinity gradient influences the habitat structure (presence of macrophytes) and the fish community (presence of large predators). Size and shape variation within and among populations was quantified by geometric morphometrics and analysed by indirect and direct gradient ordinations, using salinity and geography as a framework. Morphological divergence was associated with the salinity gradient. The evolutionary allometries observed were independent of within-group static allometries. Sexually dimorphic patterns were observed in size variation and within-population allometries. Specimens from freshwater (higher predation) sites presented smaller sizes, relatively longer caudal regions, lower anterior regions and a ventrally displaced eye. These features are consistent with an ecomorphological paradigm for aquatic organisms from populations subject to intense predation. A process of directional selection is postulated as the most likely force driving diversification among P. vivipara populations. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 93, 799–812.