Phenotypic variation plays a critical role in determining the structural organisation and ecological function of wild populations. Animal groups are often structured according to factors such as species, sex, body size and parasite load, but it is unclear whether body shape also influences patterns of social organisation, and thus contributes to population phenotypic structure. Here, we use geometric morphometric analyses to determine whether wild-caught shoals of a freshwater fish, the western rainbowfish (Melanotaenia australis), are structured according to body size and shape. Using randomisation analyses, we show that the level of variation in size and shape observed in natural group assemblages is lower than that expected under a null model of random shoal composition. In addition, we found evidence of further phenotypic structuring along an upstream-downstream environmental gradient. The putative benefits of morphological assortment include a reduction in predation risk (due to prey oddity and predator confusion effects) and increased hydrodynamic or foraging efficiency. We suggest that morphological variation is a neglected component of population social organisation that can affect population processes, such as patterns of gene flow, and ecological interactions, such as predator-prey dynamics.