Cichlid fishes are known for their adaptive radiations with prolific speciation, but also for their substantial intraspecific polymorphism and phenotypic plasticity. The Amphilophus citrinellus species complex from lakes of Nicaragua has been studied extensively as an example of trophic and colour polymorphism and possible sympatric speciation. We use the methods of geometric morphometrics to investigate variation in body shape in this species complex. There is significant shape variation between the widespread A. citrinellus and the more locally distributed A. labiatus and A. zaliosus, which shows patterns that are consistent with the taxonomic descriptions of those taxa. Contrary to the expectations from models of adaptive character divergence, the shape differences between species in analyses restricted to populations occurring syntopically are smaller than the corresponding differences computed from samples pooled over all locations. Within A. citrinellus, there is considerable variation among lakes as well as between the alternative colour and trophic morphs, suggesting local differentiation based on genetic and ecophenotypic mechanisms. © 2003 The Linnean Society of London, Biological Journal of the Linnean Society, 2003, 80, 397–408.