Most aphid species (Hemiptera : Aphididae) are parthenogenetic between periods of sexual reproduction. They are also highly polyphenic, with different adult morphs occurring in the life cycle, viz. winged, wingless, asexual and sexual. It is assumed that aphids born in a parthenogenetic clonal lineage are genetically identical regardless of the final adult form (with the exception of sexual forms). Using the randomly amplified polymorphic DNA–polymerase chain reaction (RAPD–PCR) we have found that different asexual adult phenotypes (winged and wingless) of some clones of two cereal aphid species (the grain aphid,Sitobion avenae (F.) and the bird–cherry aphid, Rhopalosiphum padi (L.)) may be distinguished by the presence or absence of one or more RAPD–PCR bands. In three of nine clones examined, such differences were found, and Southern blotting and hybridization of the discriminating bands confirmed these to be of aphid origin, rather than due to endosymbiotic bacteria or contaminating fungi. The main 248 and 296 bp bands, in the two species, respectively, were sequenced and found to be A/T rich. The smaller band showed 57 per cent homology with white striated muscle over a stretch of 90 bp. Genomic DNA treated with dimethyl sulphoxide to remove secondary structures still showed differences in RAPD–PCR profiles between winged and wingless morphs within the unusual clones. This discovery may be widespread and therefore it is important to understand the phenomenon in relation to clonal organisms.