A contact zone between Heliconius erato and H. himera in southern Ecuador provides an opportunity to study the transition from races to species in Heliconiine butterflies. Genetic differentiation at 30 allozyme loci (D = 0.28) is five times greater between himera and erato than among races of erato (D0.062). Analysis of restriction fragment length polymorphisms in an 800-bp region of the mitochondrial genome shows fixed differences between the species. Despite 5–10 per cent hybridization per generation, these mtDNA, allozyme and colour pattern differences are in almost complete linkage disequilibrium throughout the contact zone. In mixed populations, there was no consistent evidence for convergence of himera and erato allozyme allele frequencies, and only four individuals out of 383 examined showed evidence for interspecific mtDNA gene flow. Linkage analysis of backcross broods showed that the 11 allozyme and two colour pattern loci, which are markedly divergent between the species, map to eight of 21 chromosomal linkage groups. Therefore, barriers to gene flow are not restricted to just a few strongly selected loci. Although analysis of population structure shows little evidence of interspecific gene flow, strong differences between allozyme loci in levels of divergence suggest that selection and gene flow may affect loci in different ways. Hybrid zones such as this, in which divergent genotypes coexist, should provide good model systems for the study of speciation.