The diadem butterfly, Hypolimnas misippus, shows various anomalies in its presumed Batesian mimetic relationship with the distasteful danaine, Danaus chrysippus. If these anomalies are to be resolved and if reports of sexual selection in female diadems are to be correctly interpreted, an understanding of the genetics of the colour pattern polymorphism is essential. In an earlier study we developed a three-locus model (the A-M-S model) for colour pattern genetics in the diadem butterfly. Here, we show that the A locus segregates for body size as well as colour pattern. It is probably a supergene with at least four loci linked in coupling. Segregation for body size confirms several aspects of the A-M-S model: the ability of different genotypes to produce the same mimetic phenotype; the presence of a suppressor allele for hindwing white; and the effects of the A locus on the forewings of mm butterflies. Differences between the genetics of colour pattern in H. misippus and its model, D. chrysippus, favour a multiple origins rather than a selective maintenance hypothesis for the evolution of mimicry. Body size differences in both sexes must play a significant but as yet unexamined role in the maintenance of colour pattern polymorphism and in sexual selection in this species.