A contact zone between Heliconius erato and H. himera in southern Ecua
dor provides an opportunity to study the transition from races to spec
ies in Heliconiine butterflies. Genetic differentiation at 30 allozyme
loci (D = 0.28) is five times greater between himera and erato than a
mong races of erato (D<0.062). Analysis of restriction fragment length
polymorphisms in an 800-bp region of the mitochondrial genome shows f
ixed differences between the species. Despite 5-10 per cent hybridizat
ion per generation, these mtDNA, allozyme and colour pattern differenc
es are in almost complete linkage disequilibrium throughout the contac
t zone. In mixed populations, there was no consistent evidence for con
vergence of himera and erato allozyme allele frequencies, and only fou
r individuals out of 383 examined showed evidence for interspecific mt
DNA gene flow. Linkage analysis of backcross broods showed that the 11
allozyme and two colour pattern loci, which are markedly divergent be
tween the species, map to eight of 21 chromosomal linkage groups. Ther
efore, 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 alloz
yme 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 th
e study of speciation.