Leaf characters of populations of the aquatic macrophyte Montrichardia linifera were studied using geometric morphometrics to compare variation with traditional circumscriptions of the two recognized species. Two hundred and ten individuals were sampled from seven populations in the delta region of the Rio Parnaíba, north-east Brazil. Six landmarks of the leaf blade were digitized from images and analysed with MorphoJ software. Procrustes-aligned configurations were studied using principal component analysis and canonical variates analysis in the pooled data and individual populations. Sinus shape variation was studied using landmark configurations of the posterior lobe basiscopic lamina. Covariation of leaf blade shape, basiscopic lamina shape, secondary vein number and petiole ligule length was investigated with partial least squares analysis. Allometry of these variables with leaf blade centroid size was investigated using multivariate regression, linear modelling and analysis of covariance. Measured variables varied continuously over the ranges previously reported for the two species. The characters of the two species morphotypes covaried and were only partly influenced by allometric effects. Symmetric shape variables predominated, but a distinctive left- and right-handed asymmetry occurred in all populations. Genetic and ecological studies are needed to investigate the significant inter-population differences further. The study offers a methodology for a broader combined morphometric/molecular investigation. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 170, 554–572.